R/cmd_batch_rnaseq_raw_read_process.R
In Kuanhao-Chao/RNASeqR: RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
Defines functions
PostRNASeqReadProcess_Bam
PostRNASeqReadProcess_Sam
PostRNASeqReadProcess
PreRNASeqReadProcess_Bam
PreRNASeqReadProcess_Sam
PreRNASeqReadProcess
RNASeqReadProcess
RNASeqReadProcess_CMD
Documented in
RNASeqReadProcess
RNASeqReadProcess_CMD
#' @title RNASeqReadProcess_CMD
#'
#' @description
#' Process raw reads for RNA-Seq workflow in background. \cr
#' This function do 5 things : \cr
#' \enumerate{
#' \item 'Hisat2' : aligns raw reads to reference genome.
#' If \code{indices.optional} in \code{RNASeqRParam} is
#' \code{FALSE}, Hisat2 indices will be created.\cr
#' \item 'Rsamtools': converts '.sam' files to '.bam' files.\cr
#' \item 'Stringtie': assembles alignments into transcript.\cr
#' \item 'Gffcompare': examines how transcripts compare with the
#' reference annotation. \cr
#' \item 'Stringtie': creates input files for ballgown, edgeR and DESeq2.\cr
#' \item raw reads count: create raw reads count for DESeq2 and edgeR \cr
#' }
#' Before running this function, \code{RNASeqEnvironmentSet_CMD()} or
#' \code{RNASeqEnvironmentSet()} must be executed successfully. \cr
#' If you want to process raw reads for the following RNA-Seq workflow
#' in R shell, please see \code{RNASeqReadProcess()} function.\cr
#'
#' @param RNASeqRParam S4 object instance of experiment-related
#' parameters
#' @param SAMtools.or.Rsamtools Default value is \code{Rsamtools}. User can set
#' to \code{SAMtools} to use command-line-based 'samtools' instead.
#' @param Hisat2.Index.run Whether to run 'HISAT2 index' step in this function
#' step. Default value is \code{TRUE}. Set \code{FALSE} to skip
#' 'HISAT2 index' step.
#' @param Hisat2.Index.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Hisat2 index step. The default is \code{"1"}
#' @param Hisat2.Index.large.index Hisat2 index terminal '--large-index' option.
#' Default value is \code{FALSE}
#' @param Hisat2.Index.local.ftab.chars Hisat2 index terminal '-t/--ftabchars'
#' option. Default value is \code{"6"}
#' @param Hisat2.Index.local.off.rate Hisat2 index terminal '--localoffrate'
#' option. Default value is \code{"3"}
#' @param Hisat2.Index.ftab.chars Hisat2 index terminal '--localftabchars'
#' option. Default value is \code{"10"}
#' @param Hisat2.Index.off.rate Hisat2 index terminal '--offrate' option.
#' Default value is \code{"4"}
#' @param Hisat2.Alignment.run Whether to run 'HISAT2 alignment' step in this
#' function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'HISAT2 alignment' step.
#' @param Hisat2.Alignment.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Hisat2 alignment step. The default is \code{"1"}
#' @param Hisat2.Alignment.skip Hisat2 alignment terminal '-s/--skip' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.trim5 Hisat2 alignment terminal '-5/--trim5' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.trim3 Hisat2 alignment terminal '-3/--trim3' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.n.ceil.1.function.type Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"L"}
#' @param Hisat2.Alignment.n.ceil.2.constant.term Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"0"}
#' @param Hisat2.Alignment.n.ceil.3.coefficient Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"0.15"}
#' @param Hisat2.Alignment.mp.MX Hisat2 alignment terminal '--mp MX' option.
#' Default value is \code{"6"}
#' @param Hisat2.Alignment.mp.MN Hisat2 alignment terminal '--mp MN' option.
#' Default value is \code{"2"}
#' @param Hisat2.Alignment.sp.MX Hisat2 alignment terminal '--sp MX' option.
#' Default value is \code{"2"}
#' @param Hisat2.Alignment.sp.MN Hisat2 alignment terminal '--sp MN' option.
#' Default value is \code{"1"}
#' @param Hisat2.Alignment.np Hisat2 alignment terminal '--np' option.
#' Default value is \code{"1"}
#' @param Hisat2.Alignment.rdg.1 Hisat2 alignment terminal '--rdg' first option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.rdg.2 Hisat2 alignment terminal '--rdg' first option.
#' Default value is \code{"3"}
#' @param Hisat2.Alignment.rfg.1 Hisat2 alignment terminal '--rfg' first option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.rfg.2 Hisat2 alignment terminal '--rfg' first option.
#' Default value is \code{"3"}
#' @param Hisat2.Alignment.score.min.1.function.type Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"L"}
#' @param Hisat2.Alignment.score.min.2.constant.term Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"0"}
#' @param Hisat2.Alignment.score.min.3.coefficient Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"-0.2"}
#' @param Hisat2.Alignment.pen.cansplice Hisat2 alignment terminal
#' '--pen-cansplice' first option. Default value is \code{"-0"}
#' @param Hisat2.Alignment.penc.noncansplice Hisat2 alignment terminal
#' '--pen-noncansplice' option. Default value is \code{"12"}
#' @param Hisat2.Alignment.pen.canintronlen.1.function.type Hisat2 alignment
#' terminal '--pen-canintronlen' first option. Default value is \code{"G"}
#' @param Hisat2.Alignment.pen.canintronlen.2.constant.term Hisat2 alignment
#' terminal '--pen-canintronlen' second option. Default value is \code{"-8"}
#' @param Hisat2.Alignment.pen.canintronlen.3.coefficient Hisat2 alignment
#' terminal '--pen-canintronlen' third option. Default value is \code{"1"}
#' @param Hisat2.Alignment.pen.noncanintronlen.1.function.type Hisat2 alignment
#' terminal '--pen-noncanintronlen' first option. Default value is \code{"G"}
#' @param Hisat2.Alignment.pen.noncanintronlen.2.constant.term Hisat2 alignment
#' terminal '--pen-noncanintronlen' second option. Default value is \code{"-8"}
#' @param Hisat2.Alignment.pen.noncanintronlen.3.coefficient Hisat2 alignment
#' terminal '--pen-noncanintronlen' third option. Default value is \code{"1"}
#' @param Hisat2.Alignment.min.intronlen Hisat2 alignment terminal
#' '--min-intronlen' option. Default value is \code{"20"}
#' @param Hisat2.Alignment.max.intronlen Hisat2 alignment terminal '--max-intronlen'
#' option. Default value is \code{"20"}
#' @param Hisat2.Alignment.rna.strandness Hisat2 alignment terminal '--rna-strandness'
#' option. Default value is \code{"None"}
#' @param Hisat2.Alignment.k Hisat2 alignment terminal '-k' option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.max.seeds Hisat2 alignment terminal '--max-seeds' option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.secondary Hisat2 alignment terminal '--secondary' option.
#' Default value is \code{"FALSE"}
#' @param Hisat2.Alignment.minins Hisat2 alignment terminal '-I/--minins' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.maxins Hisat2 alignment terminal '-X/--maxins' option.
#' Default value is \code{"500"}
#' @param Hisat2.Alignment.seed Hisat2 alignment terminal '-X/--maxins' option.
#' Default value is \code{"0"}
#' @param STAR.Index.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for STAR index step. The default is \code{"1"}
#' @param STAR.Index.sjdbOverhang.Read.length STAR index terminal
#' '--sjdbOverhang' option. Default value is \code{"100"}
#' @param STAR.Index.genomeSAindexNbases STAR index terminal
#' '--genomeSAindexNbases' option. Default value is \code{"14"}
#' @param STAR.Index.genomeChrBinNbits STAR index terminal
#' '--genomeChrBinNbits' option. Default value is \code{"18"}
#' @param STAR.Index.genomeSAsparseD STAR index terminal
#' '--genomeSAsparseD' option. Default value is \code{"1"}
#' @param STAR.Alignment.run Whether to run 'STAR index' step in this function
#' step. Default value is \code{FALSE}. Set \code{TRUE} to run STAR alignment step.
#' (need to set Hisat2.Index.run to \code{FALSE})
#' @param STAR.Alignment.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for STAR alignment step. The default is \code{"1"}
#' @param STAR.Alignment.genomeLoad STAR alignment terminal '--genomeLoad'
#' option. Default value is \code{"NoSharedMemory"}
#' @param STAR.Alignment.readMapNumber STAR alignment terminal '--readMapNumber'
#' option. Default value is \code{"-1"}
#' @param STAR.Alignment.clip3pNbases STAR alignment terminal '--clip3pNbases'
#' option. Default value is \code{"0"}
#' @param STAR.Alignment.clip5pNbases STAR alignment terminal '--clip5pNbases'
#' option. Default value is \code{"0"}
#' @param STAR.Alignment.clip3pAdapterSeq STAR alignment terminal '--clip3pAdapterSeq'
#' option. Default value is \code{"-"}
#' @param STAR.Alignment.clip3pAdapterMMp STAR alignment terminal '--clip3pAdapterMMp'
#' option. Default value is \code{"0.1"}
#' @param STAR.Alignment.clip3pAfterAdapterNbases STAR alignment terminal
#' '--clip3pAfterAdapterNbases' option. Default value is \code{"0"}
#' @param STAR.Alignment.limitGenomeGenerateRAM STAR alignment terminal
#' '--limitGenomeGenerateRAM' option. Default value is \code{"31000000000"}
#' @param STAR.Alignment.limitIObufferSize STAR alignment terminal
#' '--limitIObufferSize' option. Default value is \code{"150000000"}
#' @param STAR.Alignment.limitOutSAMoneReadBytes STAR alignment terminal
#' '--limitOutSAMoneReadBytes' option. Default value is \code{"100000"}
#' @param STAR.Alignment.limitOutSJoneRead STAR alignment terminal
#' '--limitOutSJoneRead' option. Default value is \code{"1000"}
#' @param STAR.Alignment.limitOutSJcollapsed STAR alignment terminal
#' '--limitOutSJcollapsed' option. Default value is \code{"1000000"}
#' @param STAR.Alignment.limitBAMsortRAM STAR alignment terminal
#' '--limitBAMsortRAM' option. Default value is \code{"0"}
#' @param STAR.Alignment.outReadsUnmapped STAR alignment terminal
#' '--outReadsUnmapped' option. Default value is \code{"None"}
#' @param STAR.Alignment.outQSconversionAdd STAR alignment terminal
#' '--outQSconversionAdd' option. Default value is \code{"0"}
#' @param STAR.Alignment.outSAMprimaryFlag STAR alignment terminal
#' '--outSAMprimaryFlag' option. Default value is \code{"OneBestScore"}
#' @param STAR.Alignment.outSAMmapqUnique STAR alignment terminal
#' '--outSAMmapqUnique' option. Default value is \code{"255"}
#' @param STAR.Alignment.scoreGap STAR alignment terminal
#' '--scoreGap' option. Default value is \code{"0"}
#' @param STAR.Alignment.scoreGapNoncan STAR alignment terminal
#' '--scoreGapNoncan' option. Default value is \code{"-8"}
#' @param STAR.Alignment.scoreGapGCAG STAR alignment terminal
#' '--scoreGapGCAG' option. Default value is \code{"-4"}
#' @param STAR.Alignment.scoreGapATAC STAR alignment terminal
#' '--scoreGapATAC' option. Default value is \code{"-8"}
#' @param STAR.Alignment.scoreGenomicLengthLog2scale STAR alignment terminal
#' '--scoreGenomicLengthLog2scale' option. Default value is \code{"-0.25"}
#' @param STAR.Alignment.scoreDelOpen STAR alignment terminal
#' '--scoreDelOpen' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreDelBase STAR alignment terminal
#' '--scoreDelBase' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreInsOpen STAR alignment terminal
#' '--scoreInsOpen' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreInsBase STAR alignment terminal
#' '--scoreInsBase' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreStitchSJshift STAR alignment terminal
#' '--scoreStitchSJshift' option. Default value is \code{"1"}
#' @param STAR.Alignment.seedSearchStartLmax STAR alignment terminal
#' '--scoreStitchSJshift' option. Default value is \code{"50"}
#' @param STAR.Alignment.seedSearchStartLmaxOverLread STAR alignment terminal
#' '--seedSearchStartLmaxOverLread' option. Default value is \code{"1.0"}
#' @param STAR.Alignment.seedSearchLmax STAR alignment terminal
#' '--seedSearchLmax' option. Default value is \code{"0"}
#' @param STAR.Alignment.seedMultimapNmax STAR alignment terminal
#' '--seedMultimapNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.seedPerReadNmax STAR alignment terminal
#' '--seedPerReadNmax' option. Default value is \code{"1000"}
#' @param STAR.Alignment.seedPerWindowNmax STAR alignment terminal
#' '--seedPerWindowNmax' option. Default value is \code{"50"}
#' @param STAR.Alignment.seedNoneLociPerWindow STAR alignment terminal
#' '--seedNoneLociPerWindow' option. Default value is \code{"10"}
#' @param STAR.Alignment.alignIntronMin STAR alignment terminal
#' '--alignIntronMin' option. Default value is \code{"21"}
#' @param STAR.Alignment.alignIntronMax STAR alignment terminal
#' '--alignIntronMax' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignMatesGapMax STAR alignment terminal
#' '--alignMatesGapMax' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignSJoverhangMin STAR alignment terminal
#' '--alignSJoverhangMin' option. Default value is \code{"5"}
#' @param STAR.Alignment.alignSJDBoverhangMin STAR alignment terminal
#' '--alignSJDBoverhangMin' option. Default value is \code{"3"}
#' @param STAR.Alignment.alignSplicedMateMapLmin STAR alignment terminal
#' '--alignSplicedMateMapLmin' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignSplicedMateMapLminOverLmate STAR alignment terminal
#' '--alignSplicedMateMapLminOverLmate' option. Default value is \code{"0.66"}
#' @param STAR.Alignment.alignWindowsPerReadNmax STAR alignment terminal
#' '--alignWindowsPerReadNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.alignTranscriptsPerWindowNmax STAR alignment terminal
#' '--alignTranscriptsPerWindowNmax' option. Default value is \code{"100"}
#' @param STAR.Alignment.alignTranscriptsPerReadNmax STAR alignment terminal
#' '--alignTranscriptsPerReadNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.alignEndsType STAR alignment terminal
#' '--alignEndsType' option. Default value is \code{"Local"}
#' @param STAR.Alignment.winAnchorMultimapNmax STAR alignment terminal
#' '--winAnchorMultimapNmax' option. Default value is \code{"50"}
#' @param STAR.Alignment.winBinNbits STAR alignment terminal
#' '--winBinNbits' option. Default value is \code{"16"}
#' @param STAR.Alignment.winAnchorDistNbins STAR alignment terminal
#' '--winAnchorDistNbins' option. Default value is \code{"9"}
#' @param STAR.Alignment.winFlankNbins STAR alignment terminal
#' '--winFlankNbins' option. Default value is \code{"4"}
#' @param Rsamtools.Bam.run Whether to run 'Rsamtools SAM to BAM' step in this
#' function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'Rsamtools SAM to BAM' step.
#' @param Samtools.Bam.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Samtools sam to bam step. The default is \code{"1"}
#' @param Rsamtools.nCores The number of cores to use when running
#' 'Rsamtools' step. Default value is \code{1}
#' @param StringTie.Assemble.run Whether to run 'StringTie assembly' step in
#' this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie assembly' step.
#' @param Stringtie.Assembly.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie assembly. The default is \code{"1"}
#' @param Stringtie.Assembly.f Stringtie assembly terminal
#' '-f' option. Default value is \code{"0.1"}
#' @param Stringtie.Assembly.m Stringtie assembly terminal
#' '-m' option. Default value is \code{"200"}
#' @param Stringtie.Assembly.c Stringtie assembly terminal
#' '-c' option. Default value is \code{"2.5"}
#' @param Stringtie.Assembly.g Stringtie assembly terminal
#' '-g' option. Default value is \code{"50"}
#' @param Stringtie.Assembly.M Stringtie assembly terminal
#' '-M' option. Default value is \code{"0.95"}
#' @param StringTie.Merge.Trans.run Whether to run 'StringTie GTF merging' step
#' in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie GTF merging' step.
#' @param Stringtie.Merge.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie merge step. The default is \code{"1"}
#' @param Gffcompare.Ref.Sample.run Whether to run 'Gffcompare comparison' step
#' in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'Gffcompare comparison' step.
#' @param StringTie.Ballgown.run Whether to run 'StringTie ballgown creation'
#' step in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie ballgown creation' step.
#' @param Stringtie.2.Ballgown.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie to ballgown step. The default is \code{"1"}
#' @param PreDECountTable.run Whether to run 'gene raw reads count creation'
#' step in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'gene raw reads count creation' step.
#' @param run Default value is \code{TRUE}. If \code{TRUE},
#' 'Rscript/Environment_Set.R' will be created and executed.
#' The output log will be stored in 'Rscript_out/Environment_Set.Rout'.
#' If \code{False}, 'Rscript/Environment_Set.R' will be
#' created without executed.
#' @param check.s4.print Default \code{TRUE}. If \code{TRUE},
#' the result of checking \code{RNASeqRParam}
#' will be reported in 'Rscript_out/Environment_Set.Rout'. If \code{FALSE},
#' the result of checking \code{RNASeqRParam} will not be in
#' 'Rscript_out/Environment_Set.Rout'.
#'
#' @return None
#' @export
#' @author Kuan-Hao Chao
#' @examples
#' data(yeast)
#' \dontrun{
#' ## Before run this function, make sure \code{RNASeqEnvironmentSet_CMD()}
#' ## (or\code{RNASeqEnvironmentSet()}) is executed successfully.
#' RNASeqReadProcess_CMD(RNASeqRParam = yeast,
#' num.parallel.threads = 10)}
#'
# Parameters: 119
RNASeqReadProcess_CMD <- function(RNASeqRParam,
SAMtools.or.Rsamtools = "Rsamtools",
Hisat2.Index.run = TRUE,
Hisat2.Index.num.parallel.threads = "1",
Hisat2.Index.large.index = FALSE,
Hisat2.Index.local.ftab.chars = "6",
Hisat2.Index.local.off.rate = "3",
Hisat2.Index.ftab.chars = "10",
Hisat2.Index.off.rate = "4",
Hisat2.Alignment.run = TRUE,
Hisat2.Alignment.num.parallel.threads = "1",
Hisat2.Alignment.skip = "0",
Hisat2.Alignment.trim5 = "0",
Hisat2.Alignment.trim3 = "0",
Hisat2.Alignment.n.ceil.1.function.type = "L",
Hisat2.Alignment.n.ceil.2.constant.term = "0",
Hisat2.Alignment.n.ceil.3.coefficient = "0.15",
Hisat2.Alignment.mp.MX = "6",
Hisat2.Alignment.mp.MN = "2",
Hisat2.Alignment.sp.MX = "2",
Hisat2.Alignment.sp.MN = "1",
Hisat2.Alignment.np = "1",
Hisat2.Alignment.rdg.1 = "5",
Hisat2.Alignment.rdg.2 = "3",
Hisat2.Alignment.rfg.1 = "5",
Hisat2.Alignment.rfg.2 = "3",
Hisat2.Alignment.score.min.1.function.type = "L",
Hisat2.Alignment.score.min.2.constant.term = "0",
Hisat2.Alignment.score.min.3.coefficient = "-0.2",
Hisat2.Alignment.pen.cansplice = "0",
Hisat2.Alignment.penc.noncansplice = "12",
Hisat2.Alignment.pen.canintronlen.1.function.type = "G",
Hisat2.Alignment.pen.canintronlen.2.constant.term = "-8",
Hisat2.Alignment.pen.canintronlen.3.coefficient = "1",
Hisat2.Alignment.pen.noncanintronlen.1.function.type = "G",
Hisat2.Alignment.pen.noncanintronlen.2.constant.term = "-8",
Hisat2.Alignment.pen.noncanintronlen.3.coefficient = "1",
Hisat2.Alignment.min.intronlen = "20",
Hisat2.Alignment.max.intronlen = "500000",
Hisat2.Alignment.rna.strandness = "None",
Hisat2.Alignment.k = "5",
Hisat2.Alignment.max.seeds = "5",
Hisat2.Alignment.secondary = FALSE,
Hisat2.Alignment.minins = "0",
Hisat2.Alignment.maxins = "500",
Hisat2.Alignment.seed = "0",
STAR.Index.num.parallel.threads = "1",
STAR.Index.sjdbOverhang.Read.length = "100",
STAR.Index.genomeSAindexNbases = "14",
STAR.Index.genomeChrBinNbits = "18",
STAR.Index.genomeSAsparseD = "1",
STAR.Alignment.run = FALSE,
STAR.Alignment.num.parallel.threads = "1",
STAR.Alignment.genomeLoad = "NoSharedMemory",
STAR.Alignment.readMapNumber = "-1",
STAR.Alignment.clip3pNbases = "0",
STAR.Alignment.clip5pNbases = "0",
STAR.Alignment.clip3pAdapterSeq = "-",
STAR.Alignment.clip3pAdapterMMp = "0.1",
STAR.Alignment.clip3pAfterAdapterNbases = "0",
STAR.Alignment.limitGenomeGenerateRAM = "31000000000",
STAR.Alignment.limitIObufferSize = "150000000",
STAR.Alignment.limitOutSAMoneReadBytes = "100000",
STAR.Alignment.limitOutSJoneRead = "1000",
STAR.Alignment.limitOutSJcollapsed = "1000000",
STAR.Alignment.limitBAMsortRAM = "0",
STAR.Alignment.outReadsUnmapped = "None",
STAR.Alignment.outQSconversionAdd = "0",
STAR.Alignment.outSAMprimaryFlag = "OneBestScore",
STAR.Alignment.outSAMmapqUnique = "255",
STAR.Alignment.scoreGap = "0",
STAR.Alignment.scoreGapNoncan = "-8",
STAR.Alignment.scoreGapGCAG = "-4",
STAR.Alignment.scoreGapATAC = "-8",
STAR.Alignment.scoreGenomicLengthLog2scale = "-0.25",
STAR.Alignment.scoreDelOpen = "-2",
STAR.Alignment.scoreDelBase = "-2",
STAR.Alignment.scoreInsOpen = "-2",
STAR.Alignment.scoreInsBase = "-2",
STAR.Alignment.scoreStitchSJshift = "1",
STAR.Alignment.seedSearchStartLmax = "50",
STAR.Alignment.seedSearchStartLmaxOverLread = "1.0",
STAR.Alignment.seedSearchLmax = "0",
STAR.Alignment.seedMultimapNmax = "10000",
STAR.Alignment.seedPerReadNmax = "1000",
STAR.Alignment.seedPerWindowNmax = "50",
STAR.Alignment.seedNoneLociPerWindow = "10",
STAR.Alignment.alignIntronMin = "21",
STAR.Alignment.alignIntronMax = "0",
STAR.Alignment.alignMatesGapMax = "0",
STAR.Alignment.alignSJoverhangMin = "5",
STAR.Alignment.alignSJDBoverhangMin = "3",
STAR.Alignment.alignSplicedMateMapLmin = "0",
STAR.Alignment.alignSplicedMateMapLminOverLmate = "0.66",
STAR.Alignment.alignWindowsPerReadNmax = "10000",
STAR.Alignment.alignTranscriptsPerWindowNmax = "100",
STAR.Alignment.alignTranscriptsPerReadNmax = "10000",
STAR.Alignment.alignEndsType = "Local",
STAR.Alignment.winAnchorMultimapNmax = "50",
STAR.Alignment.winBinNbits = "16",
STAR.Alignment.winAnchorDistNbins = "9",
STAR.Alignment.winFlankNbins = "4",
Rsamtools.Bam.run = TRUE,
Samtools.Bam.num.parallel.threads = "1",
Rsamtools.nCores = "1",
StringTie.Assemble.run = TRUE,
Stringtie.Assembly.num.parallel.threads = "1",
Stringtie.Assembly.f = "0.1",
Stringtie.Assembly.m = "200",
Stringtie.Assembly.c = "2.5",
Stringtie.Assembly.g = "50",
Stringtie.Assembly.M = "0.95",
StringTie.Merge.Trans.run = TRUE,
Stringtie.Merge.num.parallel.threads = "1",
Gffcompare.Ref.Sample.run = TRUE,
StringTie.Ballgown.run = TRUE,
Stringtie.2.Ballgown.num.parallel.threads = "1",
PreDECountTable.run = TRUE,
run = TRUE,
check.s4.print = TRUE) {
which.s4.object <- CheckS4Object_All(RNASeqRParam, check.s4.print)
CheckOperatingSystem(FALSE)
path.prefix <- "@"(RNASeqRParam, path.prefix)
INSIDE.path.prefix <- "@"(RNASeqRParam, path.prefix)
saveRDS(RNASeqRParam,
file = paste0(INSIDE.path.prefix,
"gene_data/RNASeqRParam.rds"))
fileConn<-file(paste0(path.prefix, "Rscript/Read_Process.R"))
first <- "library(RNASeqR)"
if (which.s4.object == "RNASeqRParam") {
} else if (which.s4.object == "RNASeqRParam_Sam") {
Hisat2.Index.run = FALSE
Hisat2.Alignment.run = FALSE
STAR.Alignment.run = FALSE
} else if (which.s4.object == "RNASeqRParam_Bam") {
Hisat2.Index.run = FALSE
Hisat2.Alignment.run = FALSE
STAR.Alignment.run = FALSE
Rsamtools.Bam.run = FALSE
}
second <- paste0("RNASeqReadProcess(RNASeqRParam = 'INSIDE'",
", which.trigger = 'INSIDE'",
", INSIDE.path.prefix = '", INSIDE.path.prefix,
"', SAMtools.or.Rsamtools ='", SAMtools.or.Rsamtools,
"', Hisat2.Index.run =", Hisat2.Index.run,
", Hisat2.Index.num.parallel.threads = '", Hisat2.Index.num.parallel.threads,
"', Hisat2.Index.large.index = ", Hisat2.Index.large.index,
", Hisat2.Index.local.ftab.chars = '", Hisat2.Index.local.ftab.chars,
"', Hisat2.Index.local.off.rate = '", Hisat2.Index.local.off.rate,
"', Hisat2.Index.ftab.chars = '", Hisat2.Index.ftab.chars,
"', Hisat2.Index.off.rate = '", Hisat2.Index.off.rate,
"', Hisat2.Alignment.run = ", Hisat2.Alignment.run,
", Hisat2.Alignment.num.parallel.threads = '", Hisat2.Alignment.num.parallel.threads,
"', Hisat2.Alignment.skip = '", Hisat2.Alignment.skip,
"', Hisat2.Alignment.trim5 = '", Hisat2.Alignment.trim5,
"', Hisat2.Alignment.trim3 = '", Hisat2.Alignment.trim3,
"', Hisat2.Alignment.n.ceil.1.function.type = '", Hisat2.Alignment.n.ceil.1.function.type,
"', Hisat2.Alignment.n.ceil.2.constant.term = '", Hisat2.Alignment.n.ceil.2.constant.term,
"', Hisat2.Alignment.n.ceil.3.coefficient = '", Hisat2.Alignment.n.ceil.3.coefficient,
"', Hisat2.Alignment.mp.MX = '", Hisat2.Alignment.mp.MX,
"', Hisat2.Alignment.mp.MN = '", Hisat2.Alignment.mp.MN,
"', Hisat2.Alignment.sp.MX = '", Hisat2.Alignment.sp.MX,
"', Hisat2.Alignment.sp.MN = '", Hisat2.Alignment.sp.MN,
"', Hisat2.Alignment.np = '", Hisat2.Alignment.np,
"', Hisat2.Alignment.rdg.1 = '", Hisat2.Alignment.rdg.1,
"', Hisat2.Alignment.rdg.2 = '", Hisat2.Alignment.rdg.2,
"', Hisat2.Alignment.rfg.1 = '", Hisat2.Alignment.rfg.1,
"', Hisat2.Alignment.rfg.2 = '", Hisat2.Alignment.rfg.2,
"', Hisat2.Alignment.score.min.1.function.type = '", Hisat2.Alignment.score.min.1.function.type,
"', Hisat2.Alignment.score.min.2.constant.term = '", Hisat2.Alignment.score.min.2.constant.term,
"', Hisat2.Alignment.score.min.3.coefficient = '", Hisat2.Alignment.score.min.3.coefficient,
"', Hisat2.Alignment.pen.cansplice = '", Hisat2.Alignment.pen.cansplice,
"', Hisat2.Alignment.penc.noncansplice = '", Hisat2.Alignment.penc.noncansplice,
"', Hisat2.Alignment.pen.canintronlen.1.function.type = '", Hisat2.Alignment.pen.canintronlen.1.function.type,
"', Hisat2.Alignment.pen.canintronlen.2.constant.term = '", Hisat2.Alignment.pen.canintronlen.2.constant.term,
"', Hisat2.Alignment.pen.canintronlen.3.coefficient = '", Hisat2.Alignment.pen.canintronlen.3.coefficient,
"', Hisat2.Alignment.pen.noncanintronlen.1.function.type = '", Hisat2.Alignment.pen.noncanintronlen.1.function.type,
"', Hisat2.Alignment.pen.noncanintronlen.2.constant.term = '", Hisat2.Alignment.pen.noncanintronlen.2.constant.term,
"', Hisat2.Alignment.pen.noncanintronlen.3.coefficient = '", Hisat2.Alignment.pen.noncanintronlen.3.coefficient,
"', Hisat2.Alignment.min.intronlen = '", Hisat2.Alignment.min.intronlen,
"', Hisat2.Alignment.max.intronlen = '", Hisat2.Alignment.max.intronlen,
"', Hisat2.Alignment.rna.strandness = '", Hisat2.Alignment.rna.strandness,
"', Hisat2.Alignment.k = '", Hisat2.Alignment.k,
"', Hisat2.Alignment.max.seeds = '", Hisat2.Alignment.max.seeds,
"', Hisat2.Alignment.secondary = ", Hisat2.Alignment.secondary,
", Hisat2.Alignment.minins = '", Hisat2.Alignment.minins,
"', Hisat2.Alignment.maxins = '", Hisat2.Alignment.maxins,
"', Hisat2.Alignment.seed = '", Hisat2.Alignment.seed,
"', STAR.Index.num.parallel.threads = '", STAR.Index.num.parallel.threads,
"', STAR.Index.sjdbOverhang.Read.length = '", STAR.Index.sjdbOverhang.Read.length,
"', STAR.Index.genomeSAindexNbases = '", STAR.Index.genomeSAindexNbases,
"', STAR.Index.genomeChrBinNbits = '", STAR.Index.genomeChrBinNbits,
"', STAR.Index.genomeSAsparseD = '", STAR.Index.genomeSAsparseD,
"', STAR.Alignment.run = ", STAR.Alignment.run,
", STAR.Alignment.num.parallel.threads = '", STAR.Alignment.num.parallel.threads,
"', STAR.Alignment.genomeLoad = '", STAR.Alignment.genomeLoad,
"', STAR.Alignment.readMapNumber = '", STAR.Alignment.readMapNumber,
"', STAR.Alignment.clip3pNbases = '", STAR.Alignment.clip3pNbases,
"', STAR.Alignment.clip5pNbases = '", STAR.Alignment.clip5pNbases,
"', STAR.Alignment.clip3pAdapterSeq = '", STAR.Alignment.clip3pAdapterSeq,
"', STAR.Alignment.clip3pAdapterMMp = '", STAR.Alignment.clip3pAdapterMMp,
"', STAR.Alignment.clip3pAfterAdapterNbases = '", STAR.Alignment.clip3pAfterAdapterNbases,
"', STAR.Alignment.limitGenomeGenerateRAM = '", STAR.Alignment.limitGenomeGenerateRAM,
"', STAR.Alignment.limitIObufferSize = '", STAR.Alignment.limitIObufferSize,
"', STAR.Alignment.limitOutSAMoneReadBytes = '", STAR.Alignment.limitOutSAMoneReadBytes,
"', STAR.Alignment.limitOutSJoneRead = '", STAR.Alignment.limitOutSJoneRead,
"', STAR.Alignment.limitOutSJcollapsed = '", STAR.Alignment.limitOutSJcollapsed,
"', STAR.Alignment.limitBAMsortRAM = '", STAR.Alignment.limitBAMsortRAM,
"', STAR.Alignment.outReadsUnmapped = '", STAR.Alignment.outReadsUnmapped,
"', STAR.Alignment.outQSconversionAdd = '", STAR.Alignment.outQSconversionAdd,
"', STAR.Alignment.outSAMprimaryFlag = '", STAR.Alignment.outSAMprimaryFlag,
"', STAR.Alignment.outSAMmapqUnique = '", STAR.Alignment.outSAMmapqUnique,
"', STAR.Alignment.scoreGap = '", STAR.Alignment.scoreGap,
"', STAR.Alignment.scoreGapNoncan = '", STAR.Alignment.scoreGapNoncan,
"', STAR.Alignment.scoreGapGCAG = '", STAR.Alignment.scoreGapGCAG,
"', STAR.Alignment.scoreGapATAC = '", STAR.Alignment.scoreGapATAC,
"', STAR.Alignment.scoreGenomicLengthLog2scale = '", STAR.Alignment.scoreGenomicLengthLog2scale,
"', STAR.Alignment.scoreDelOpen = '", STAR.Alignment.scoreDelOpen,
"', STAR.Alignment.scoreDelBase = '", STAR.Alignment.scoreDelBase,
"', STAR.Alignment.scoreInsOpen = '", STAR.Alignment.scoreInsOpen,
"', STAR.Alignment.scoreInsBase = '", STAR.Alignment.scoreInsBase,
"', STAR.Alignment.scoreStitchSJshift = '", STAR.Alignment.scoreStitchSJshift,
"', STAR.Alignment.seedSearchStartLmax = '", STAR.Alignment.seedSearchStartLmax,
"', STAR.Alignment.seedSearchStartLmaxOverLread = '", STAR.Alignment.seedSearchStartLmaxOverLread,
"', STAR.Alignment.seedSearchLmax = '", STAR.Alignment.seedSearchLmax,
"', STAR.Alignment.seedMultimapNmax = '", STAR.Alignment.seedMultimapNmax,
"', STAR.Alignment.seedPerReadNmax = '", STAR.Alignment.seedPerReadNmax,
"', STAR.Alignment.seedPerWindowNmax = '", STAR.Alignment.seedPerWindowNmax,
"', STAR.Alignment.seedNoneLociPerWindow = '", STAR.Alignment.seedNoneLociPerWindow,
"', STAR.Alignment.alignIntronMin = '", STAR.Alignment.alignIntronMin,
"', STAR.Alignment.alignIntronMax = '", STAR.Alignment.alignIntronMax,
"', STAR.Alignment.alignMatesGapMax = '", STAR.Alignment.alignMatesGapMax,
"', STAR.Alignment.alignSJoverhangMin = '", STAR.Alignment.alignSJoverhangMin,
"', STAR.Alignment.alignSJDBoverhangMin = '", STAR.Alignment.alignSJDBoverhangMin,
"', STAR.Alignment.alignSplicedMateMapLmin = '", STAR.Alignment.alignSplicedMateMapLmin,
"', STAR.Alignment.alignSplicedMateMapLminOverLmate = '", STAR.Alignment.alignSplicedMateMapLminOverLmate,
"', STAR.Alignment.alignWindowsPerReadNmax = '", STAR.Alignment.alignWindowsPerReadNmax,
"', STAR.Alignment.alignTranscriptsPerWindowNmax = '", STAR.Alignment.alignTranscriptsPerWindowNmax,
"', STAR.Alignment.alignTranscriptsPerReadNmax = '", STAR.Alignment.alignTranscriptsPerReadNmax,
"', STAR.Alignment.alignEndsType = '", STAR.Alignment.alignEndsType,
"', STAR.Alignment.winAnchorMultimapNmax = '", STAR.Alignment.winAnchorMultimapNmax,
"', STAR.Alignment.winBinNbits = '", STAR.Alignment.winBinNbits,
"', STAR.Alignment.winAnchorDistNbins = '", STAR.Alignment.winAnchorDistNbins,
"', STAR.Alignment.winFlankNbins = '", STAR.Alignment.winFlankNbins,
"', Rsamtools.Bam.run = ", Rsamtools.Bam.run,
", Samtools.Bam.num.parallel.threads = '", Samtools.Bam.num.parallel.threads,
"', Rsamtools.nCores = '", Rsamtools.nCores,
"', StringTie.Assemble.run = ", StringTie.Assemble.run,
", Stringtie.Assembly.num.parallel.threads = '", Stringtie.Assembly.num.parallel.threads,
"', Stringtie.Assembly.f = '", Stringtie.Assembly.f,
"', Stringtie.Assembly.m = '", Stringtie.Assembly.m,
"', Stringtie.Assembly.c = '", Stringtie.Assembly.c,
"', Stringtie.Assembly.g = '", Stringtie.Assembly.g,
"', Stringtie.Assembly.M = '", Stringtie.Assembly.M,
"', StringTie.Merge.Trans.run = ", StringTie.Merge.Trans.run,
", Stringtie.Merge.num.parallel.threads = '", Stringtie.Merge.num.parallel.threads,
"', Gffcompare.Ref.Sample.run = ", Gffcompare.Ref.Sample.run,
", StringTie.Ballgown.run = ", StringTie.Ballgown.run,
", Stringtie.2.Ballgown.num.parallel.threads = '", Stringtie.2.Ballgown.num.parallel.threads,
"', PreDECountTable.run = ", PreDECountTable.run,
", check.s4.print = ", check.s4.print, ")")
writeLines(c(first, second), fileConn)
close(fileConn)
message("\u2605 '", path.prefix,
"Rscript/Read_Process.R' has been created.\n")
if (run) {
R.home.lib <- R.home()
R.home.bin <- gsub("/lib/R", "/bin/R", R.home.lib)
system2(command = "nohup",
args = paste0(R.home.bin, " CMD BATCH ",
path.prefix,
"Rscript/Read_Process.R ", path.prefix,
"Rscript_out/Read_Process.Rout"),
stdout = "",
wait = FALSE)
message("\u2605 RNASeq alignment, assembly, quantification, ",
"mergence, comparison, reads process are doing in the ",
"background. Check current progress in '", path.prefix,
"Rscript_out/Read_Process.Rout'\n\n")
}
}
#' @title RNASeqReadProcess
#'
#' @description
#' Process raw reads for RNA-Seq workflow in R shell \cr
#' This function do 5 things : \cr
#' \enumerate{
#' \item 'Hisat2' : aligns raw reads to reference genome.
#' If \code{indices.optional} in \code{RNASeqRParam} is
#' \code{FALSE}, Hisat2 indices will be created.\cr
#' \item 'Rsamtools': converts '.sam' files to '.bam' files.\cr
#' \item 'Stringtie': assembles alignments into transcript.\cr
#' \item 'Gffcompare': examines how transcripts compare with the
#' reference annotation. \cr
#' \item 'Stringtie': creates input files for ballgown, edgeR and DESeq2.\cr
#' \item raw reads count: create raw reads count for DESeq2 and edgeR \cr
#' }
#' Before running this function, \code{RNASeqEnvironmentSet_CMD()} or
#' \code{RNASeqEnvironmentSet()} must be executed successfully.
#' If you want to process raw reads for the following RNA-Seq workflow in
#' background, please see \code{RNASeqReadProcess_CMD()} function.
#'
#' @param RNASeqRParam S4 object instance of experiment-related
#' parameters
#' @param which.trigger Default value is \code{OUTSIDE}. User should not change
#' this value.
#' @param INSIDE.path.prefix Default value is \code{NA}. User should not change
#' this value.
#' @param SAMtools.or.Rsamtools Default value is \code{Rsamtools}. User can set
#' to \code{SAMtools} to use command-line-based 'samtools' instead.
#' @param Hisat2.Index.run Whether to run 'HISAT2 index' step in this function
#' step. Default value is \code{TRUE}. Set \code{FALSE} to skip
#' 'HISAT2 index' step.
#' @param Hisat2.Index.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Hisat2 index step. The default is \code{"1"}
#' @param Hisat2.Index.large.index Hisat2 index terminal '--large-index' option.
#' Default value is \code{FALSE}
#' @param Hisat2.Index.local.ftab.chars Hisat2 index terminal '-t/--ftabchars'
#' option. Default value is \code{"6"}
#' @param Hisat2.Index.local.off.rate Hisat2 index terminal '--localoffrate'
#' option. Default value is \code{"3"}
#' @param Hisat2.Index.ftab.chars Hisat2 index terminal '--localftabchars'
#' option. Default value is \code{"10"}
#' @param Hisat2.Index.off.rate Hisat2 index terminal '--offrate' option.
#' Default value is \code{"4"}
#' @param Hisat2.Alignment.run Whether to run 'HISAT2 alignment' step in this
#' function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'HISAT2 alignment' step.
#' @param Hisat2.Alignment.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Hisat2 alignment step. The default is \code{"1"}
#' @param Hisat2.Alignment.skip Hisat2 alignment terminal '-s/--skip' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.trim5 Hisat2 alignment terminal '-5/--trim5' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.trim3 Hisat2 alignment terminal '-3/--trim3' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.n.ceil.1.function.type Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"L"}
#' @param Hisat2.Alignment.n.ceil.2.constant.term Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"0"}
#' @param Hisat2.Alignment.n.ceil.3.coefficient Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"0.15"}
#' @param Hisat2.Alignment.mp.MX Hisat2 alignment terminal '--mp MX' option.
#' Default value is \code{"6"}
#' @param Hisat2.Alignment.mp.MN Hisat2 alignment terminal '--mp MN' option.
#' Default value is \code{"2"}
#' @param Hisat2.Alignment.sp.MX Hisat2 alignment terminal '--sp MX' option.
#' Default value is \code{"2"}
#' @param Hisat2.Alignment.sp.MN Hisat2 alignment terminal '--sp MN' option.
#' Default value is \code{"1"}
#' @param Hisat2.Alignment.np Hisat2 alignment terminal '--np' option.
#' Default value is \code{"1"}
#' @param Hisat2.Alignment.rdg.1 Hisat2 alignment terminal '--rdg' first option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.rdg.2 Hisat2 alignment terminal '--rdg' first option.
#' Default value is \code{"3"}
#' @param Hisat2.Alignment.rfg.1 Hisat2 alignment terminal '--rfg' first option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.rfg.2 Hisat2 alignment terminal '--rfg' first option.
#' Default value is \code{"3"}
#' @param Hisat2.Alignment.score.min.1.function.type Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"L"}
#' @param Hisat2.Alignment.score.min.2.constant.term Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"0"}
#' @param Hisat2.Alignment.score.min.3.coefficient Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"-0.2"}
#' @param Hisat2.Alignment.pen.cansplice Hisat2 alignment terminal
#' '--pen-cansplice' first option. Default value is \code{"-0"}
#' @param Hisat2.Alignment.penc.noncansplice Hisat2 alignment terminal
#' '--pen-noncansplice' option. Default value is \code{"12"}
#' @param Hisat2.Alignment.pen.canintronlen.1.function.type Hisat2 alignment
#' terminal '--pen-canintronlen' first option. Default value is \code{"G"}
#' @param Hisat2.Alignment.pen.canintronlen.2.constant.term Hisat2 alignment
#' terminal '--pen-canintronlen' second option. Default value is \code{"-8"}
#' @param Hisat2.Alignment.pen.canintronlen.3.coefficient Hisat2 alignment
#' terminal '--pen-canintronlen' third option. Default value is \code{"1"}
#' @param Hisat2.Alignment.pen.noncanintronlen.1.function.type Hisat2 alignment
#' terminal '--pen-noncanintronlen' first option. Default value is \code{"G"}
#' @param Hisat2.Alignment.pen.noncanintronlen.2.constant.term Hisat2 alignment
#' terminal '--pen-noncanintronlen' second option. Default value is \code{"-8"}
#' @param Hisat2.Alignment.pen.noncanintronlen.3.coefficient Hisat2 alignment
#' terminal '--pen-noncanintronlen' third option. Default value is \code{"1"}
#' @param Hisat2.Alignment.min.intronlen Hisat2 alignment terminal
#' '--min-intronlen' option. Default value is \code{"20"}
#' @param Hisat2.Alignment.max.intronlen Hisat2 alignment terminal '--max-intronlen'
#' option. Default value is \code{"20"}
#' @param Hisat2.Alignment.rna.strandness Hisat2 alignment terminal '--rna-strandness'
#' option. Default value is \code{"None"}
#' @param Hisat2.Alignment.k Hisat2 alignment terminal '-k' option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.max.seeds Hisat2 alignment terminal '--max-seeds' option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.secondary Hisat2 alignment terminal '--secondary' option.
#' Default value is \code{"FALSE"}
#' @param Hisat2.Alignment.minins Hisat2 alignment terminal '-I/--minins' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.maxins Hisat2 alignment terminal '-X/--maxins' option.
#' Default value is \code{"500"}
#' @param Hisat2.Alignment.seed Hisat2 alignment terminal '-X/--maxins' option.
#' Default value is \code{"0"}
#' @param STAR.Index.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for STAR index step. The default is \code{"1"}
#' @param STAR.Index.sjdbOverhang.Read.length STAR index terminal
#' '--sjdbOverhang' option. Default value is \code{"100"}
#' @param STAR.Index.genomeSAindexNbases STAR index terminal
#' '--genomeSAindexNbases' option. Default value is \code{"14"}
#' @param STAR.Index.genomeChrBinNbits STAR index terminal
#' '--genomeChrBinNbits' option. Default value is \code{"18"}
#' @param STAR.Index.genomeSAsparseD STAR index terminal
#' '--genomeSAsparseD' option. Default value is \code{"1"}
#' @param STAR.Alignment.run Whether to run 'STAR index' step in this function
#' step. Default value is \code{FALSE}. Set \code{TRUE} to run STAR alignment step.
#' (need to set Hisat2.Index.run to \code{FALSE})
#' @param STAR.Alignment.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for STAR alignment step. The default is \code{"1"}
#' @param STAR.Alignment.genomeLoad STAR alignment terminal '--genomeLoad'
#' option. Default value is \code{"NoSharedMemory"}
#' @param STAR.Alignment.readMapNumber STAR alignment terminal '--readMapNumber'
#' option. Default value is \code{"-1"}
#' @param STAR.Alignment.clip3pNbases STAR alignment terminal '--clip3pNbases'
#' option. Default value is \code{"0"}
#' @param STAR.Alignment.clip5pNbases STAR alignment terminal '--clip5pNbases'
#' option. Default value is \code{"0"}
#' @param STAR.Alignment.clip3pAdapterSeq STAR alignment terminal '--clip3pAdapterSeq'
#' option. Default value is \code{"-"}
#' @param STAR.Alignment.clip3pAdapterMMp STAR alignment terminal '--clip3pAdapterMMp'
#' option. Default value is \code{"0.1"}
#' @param STAR.Alignment.clip3pAfterAdapterNbases STAR alignment terminal
#' '--clip3pAfterAdapterNbases' option. Default value is \code{"0"}
#' @param STAR.Alignment.limitGenomeGenerateRAM STAR alignment terminal
#' '--limitGenomeGenerateRAM' option. Default value is \code{"31000000000"}
#' @param STAR.Alignment.limitIObufferSize STAR alignment terminal
#' '--limitIObufferSize' option. Default value is \code{"150000000"}
#' @param STAR.Alignment.limitOutSAMoneReadBytes STAR alignment terminal
#' '--limitOutSAMoneReadBytes' option. Default value is \code{"100000"}
#' @param STAR.Alignment.limitOutSJoneRead STAR alignment terminal
#' '--limitOutSJoneRead' option. Default value is \code{"1000"}
#' @param STAR.Alignment.limitOutSJcollapsed STAR alignment terminal
#' '--limitOutSJcollapsed' option. Default value is \code{"1000000"}
#' @param STAR.Alignment.limitBAMsortRAM STAR alignment terminal
#' '--limitBAMsortRAM' option. Default value is \code{"0"}
#' @param STAR.Alignment.outReadsUnmapped STAR alignment terminal
#' '--outReadsUnmapped' option. Default value is \code{"None"}
#' @param STAR.Alignment.outQSconversionAdd STAR alignment terminal
#' '--outQSconversionAdd' option. Default value is \code{"0"}
#' @param STAR.Alignment.outSAMprimaryFlag STAR alignment terminal
#' '--outSAMprimaryFlag' option. Default value is \code{"OneBestScore"}
#' @param STAR.Alignment.outSAMmapqUnique STAR alignment terminal
#' '--outSAMmapqUnique' option. Default value is \code{"255"}
#' @param STAR.Alignment.scoreGap STAR alignment terminal
#' '--scoreGap' option. Default value is \code{"0"}
#' @param STAR.Alignment.scoreGapNoncan STAR alignment terminal
#' '--scoreGapNoncan' option. Default value is \code{"-8"}
#' @param STAR.Alignment.scoreGapGCAG STAR alignment terminal
#' '--scoreGapGCAG' option. Default value is \code{"-4"}
#' @param STAR.Alignment.scoreGapATAC STAR alignment terminal
#' '--scoreGapATAC' option. Default value is \code{"-8"}
#' @param STAR.Alignment.scoreGenomicLengthLog2scale STAR alignment terminal
#' '--scoreGenomicLengthLog2scale' option. Default value is \code{"-0.25"}
#' @param STAR.Alignment.scoreDelOpen STAR alignment terminal
#' '--scoreDelOpen' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreDelBase STAR alignment terminal
#' '--scoreDelBase' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreInsOpen STAR alignment terminal
#' '--scoreInsOpen' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreInsBase STAR alignment terminal
#' '--scoreInsBase' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreStitchSJshift STAR alignment terminal
#' '--scoreStitchSJshift' option. Default value is \code{"1"}
#' @param STAR.Alignment.seedSearchStartLmax STAR alignment terminal
#' '--scoreStitchSJshift' option. Default value is \code{"50"}
#' @param STAR.Alignment.seedSearchStartLmaxOverLread STAR alignment terminal
#' '--seedSearchStartLmaxOverLread' option. Default value is \code{"1.0"}
#' @param STAR.Alignment.seedSearchLmax STAR alignment terminal
#' '--seedSearchLmax' option. Default value is \code{"0"}
#' @param STAR.Alignment.seedMultimapNmax STAR alignment terminal
#' '--seedMultimapNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.seedPerReadNmax STAR alignment terminal
#' '--seedPerReadNmax' option. Default value is \code{"1000"}
#' @param STAR.Alignment.seedPerWindowNmax STAR alignment terminal
#' '--seedPerWindowNmax' option. Default value is \code{"50"}
#' @param STAR.Alignment.seedNoneLociPerWindow STAR alignment terminal
#' '--seedNoneLociPerWindow' option. Default value is \code{"10"}
#' @param STAR.Alignment.alignIntronMin STAR alignment terminal
#' '--alignIntronMin' option. Default value is \code{"21"}
#' @param STAR.Alignment.alignIntronMax STAR alignment terminal
#' '--alignIntronMax' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignMatesGapMax STAR alignment terminal
#' '--alignMatesGapMax' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignSJoverhangMin STAR alignment terminal
#' '--alignSJoverhangMin' option. Default value is \code{"5"}
#' @param STAR.Alignment.alignSJDBoverhangMin STAR alignment terminal
#' '--alignSJDBoverhangMin' option. Default value is \code{"3"}
#' @param STAR.Alignment.alignSplicedMateMapLmin STAR alignment terminal
#' '--alignSplicedMateMapLmin' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignSplicedMateMapLminOverLmate STAR alignment terminal
#' '--alignSplicedMateMapLminOverLmate' option. Default value is \code{"0.66"}
#' @param STAR.Alignment.alignWindowsPerReadNmax STAR alignment terminal
#' '--alignWindowsPerReadNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.alignTranscriptsPerWindowNmax STAR alignment terminal
#' '--alignTranscriptsPerWindowNmax' option. Default value is \code{"100"}
#' @param STAR.Alignment.alignTranscriptsPerReadNmax STAR alignment terminal
#' '--alignTranscriptsPerReadNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.alignEndsType STAR alignment terminal
#' '--alignEndsType' option. Default value is \code{"Local"}
#' @param STAR.Alignment.winAnchorMultimapNmax STAR alignment terminal
#' '--winAnchorMultimapNmax' option. Default value is \code{"50"}
#' @param STAR.Alignment.winBinNbits STAR alignment terminal
#' '--winBinNbits' option. Default value is \code{"16"}
#' @param STAR.Alignment.winAnchorDistNbins STAR alignment terminal
#' '--winAnchorDistNbins' option. Default value is \code{"9"}
#' @param STAR.Alignment.winFlankNbins STAR alignment terminal
#' '--winFlankNbins' option. Default value is \code{"4"}
#' @param Rsamtools.Bam.run Whether to run 'Rsamtools SAM to BAM' step in this
#' function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'Rsamtools SAM to BAM' step.
#' @param Samtools.Bam.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Samtools sam to bam step. The default is \code{"1"}
#' @param Rsamtools.nCores The number of cores to use when running
#' 'Rsamtools' step. Default value is \code{1}
#' @param StringTie.Assemble.run Whether to run 'StringTie assembly' step in
#' this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie assembly' step.
#' @param Stringtie.Assembly.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie assembly. The default is \code{"1"}
#' @param Stringtie.Assembly.f Stringtie assembly terminal
#' '-f' option. Default value is \code{"0.1"}
#' @param Stringtie.Assembly.m Stringtie assembly terminal
#' '-m' option. Default value is \code{"200"}
#' @param Stringtie.Assembly.c Stringtie assembly terminal
#' '-c' option. Default value is \code{"2.5"}
#' @param Stringtie.Assembly.g Stringtie assembly terminal
#' '-g' option. Default value is \code{"50"}
#' @param Stringtie.Assembly.M Stringtie assembly terminal
#' '-M' option. Default value is \code{"0.95"}
#' @param StringTie.Merge.Trans.run Whether to run 'StringTie GTF merging' step
#' in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie GTF merging' step.
#' @param Stringtie.Merge.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie merge step. The default is \code{"1"}
#' @param Gffcompare.Ref.Sample.run Whether to run 'Gffcompare comparison' step
#' in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'Gffcompare comparison' step.
#' @param StringTie.Ballgown.run Whether to run 'StringTie ballgown creation'
#' step in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie ballgown creation' step.
#' @param Stringtie.2.Ballgown.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie to ballgown step. The default is \code{"1"}
#' @param PreDECountTable.run Whether to run 'gene raw reads count creation'
#' step in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'gene raw reads count creation' step.
#' @param check.s4.print Default \code{TRUE}. If \code{TRUE},
#' the result of checking \code{RNASeqRParam}
#' will be reported in 'Rscript_out/Environment_Set.Rout'. If \code{FALSE},
#' the result of checking \code{RNASeqRParam} will not be in
#' 'Rscript_out/Environment_Set.Rout'.
#'
#' @return None
#' @export
#' @author Kuan-Hao Chao
#' @examples
#' data(yeast)
#' \dontrun{
#' ## Before run this function, make sure \code{RNASeqEnvironmentSet_CMD()}
#' ##(or\code{RNASeqEnvironmentSet()}) is executed successfully.
#' RNASeqReadProcess(RNASeqRParam = yeast,
#' num.parallel.threads = 10)}
# Parameters: 120
RNASeqReadProcess <- function(RNASeqRParam,
which.trigger = "OUTSIDE",
INSIDE.path.prefix = NA,
SAMtools.or.Rsamtools = "Rsamtools",
Hisat2.Index.run = TRUE,
Hisat2.Index.num.parallel.threads = "1",
Hisat2.Index.large.index = FALSE,
Hisat2.Index.local.ftab.chars = "6",
Hisat2.Index.local.off.rate = "3",
Hisat2.Index.ftab.chars = "10",
Hisat2.Index.off.rate = "4",
Hisat2.Alignment.run = TRUE,
Hisat2.Alignment.num.parallel.threads = "1",
Hisat2.Alignment.skip = "0",
Hisat2.Alignment.trim5 = "0",
Hisat2.Alignment.trim3 = "0",
Hisat2.Alignment.n.ceil.1.function.type = "L",
Hisat2.Alignment.n.ceil.2.constant.term = "0",
Hisat2.Alignment.n.ceil.3.coefficient = "0.15",
Hisat2.Alignment.mp.MX = "6",
Hisat2.Alignment.mp.MN = "2",
Hisat2.Alignment.sp.MX = "2",
Hisat2.Alignment.sp.MN = "1",
Hisat2.Alignment.np = "1",
Hisat2.Alignment.rdg.1 = "5",
Hisat2.Alignment.rdg.2 = "3",
Hisat2.Alignment.rfg.1 = "5",
Hisat2.Alignment.rfg.2 = "3",
Hisat2.Alignment.score.min.1.function.type = "L",
Hisat2.Alignment.score.min.2.constant.term = "0",
Hisat2.Alignment.score.min.3.coefficient = "-0.2",
Hisat2.Alignment.pen.cansplice = "0",
Hisat2.Alignment.penc.noncansplice = "12",
Hisat2.Alignment.pen.canintronlen.1.function.type = "G",
Hisat2.Alignment.pen.canintronlen.2.constant.term = "-8",
Hisat2.Alignment.pen.canintronlen.3.coefficient = "1",
Hisat2.Alignment.pen.noncanintronlen.1.function.type = "G",
Hisat2.Alignment.pen.noncanintronlen.2.constant.term = "-8",
Hisat2.Alignment.pen.noncanintronlen.3.coefficient = "1",
Hisat2.Alignment.min.intronlen = "20",
Hisat2.Alignment.max.intronlen = "500000",
Hisat2.Alignment.rna.strandness = "None",
Hisat2.Alignment.k = "5",
Hisat2.Alignment.max.seeds = "5",
Hisat2.Alignment.secondary = FALSE,
Hisat2.Alignment.minins = "0",
Hisat2.Alignment.maxins = "500",
Hisat2.Alignment.seed = "0",
STAR.Index.num.parallel.threads = "1",
STAR.Index.sjdbOverhang.Read.length = "100",
STAR.Index.genomeSAindexNbases = "14",
STAR.Index.genomeChrBinNbits = "18",
STAR.Index.genomeSAsparseD = "1",
STAR.Alignment.run = FALSE,
STAR.Alignment.num.parallel.threads = "1",
STAR.Alignment.genomeLoad = "NoSharedMemory",
STAR.Alignment.readMapNumber = "-1",
STAR.Alignment.clip3pNbases = "0",
STAR.Alignment.clip5pNbases = "0",
STAR.Alignment.clip3pAdapterSeq = "-",
STAR.Alignment.clip3pAdapterMMp = "0.1",
STAR.Alignment.clip3pAfterAdapterNbases = "0",
STAR.Alignment.limitGenomeGenerateRAM = "31000000000",
STAR.Alignment.limitIObufferSize = "150000000",
STAR.Alignment.limitOutSAMoneReadBytes = "100000",
STAR.Alignment.limitOutSJoneRead = "1000",
STAR.Alignment.limitOutSJcollapsed = "1000000",
STAR.Alignment.limitBAMsortRAM = "0",
STAR.Alignment.outReadsUnmapped = "None",
STAR.Alignment.outQSconversionAdd = "0",
STAR.Alignment.outSAMprimaryFlag = "OneBestScore",
STAR.Alignment.outSAMmapqUnique = "255",
STAR.Alignment.scoreGap = "0",
STAR.Alignment.scoreGapNoncan = "-8",
STAR.Alignment.scoreGapGCAG = "-4",
STAR.Alignment.scoreGapATAC = "-8",
STAR.Alignment.scoreGenomicLengthLog2scale = "-0.25",
STAR.Alignment.scoreDelOpen = "-2",
STAR.Alignment.scoreDelBase = "-2",
STAR.Alignment.scoreInsOpen = "-2",
STAR.Alignment.scoreInsBase = "-2",
STAR.Alignment.scoreStitchSJshift = "1",
STAR.Alignment.seedSearchStartLmax = "50",
STAR.Alignment.seedSearchStartLmaxOverLread = "1.0",
STAR.Alignment.seedSearchLmax = "0",
STAR.Alignment.seedMultimapNmax = "10000",
STAR.Alignment.seedPerReadNmax = "1000",
STAR.Alignment.seedPerWindowNmax = "50",
STAR.Alignment.seedNoneLociPerWindow = "10",
STAR.Alignment.alignIntronMin = "21",
STAR.Alignment.alignIntronMax = "0",
STAR.Alignment.alignMatesGapMax = "0",
STAR.Alignment.alignSJoverhangMin = "5",
STAR.Alignment.alignSJDBoverhangMin = "3",
STAR.Alignment.alignSplicedMateMapLmin = "0",
STAR.Alignment.alignSplicedMateMapLminOverLmate = "0.66",
STAR.Alignment.alignWindowsPerReadNmax = "10000",
STAR.Alignment.alignTranscriptsPerWindowNmax = "100",
STAR.Alignment.alignTranscriptsPerReadNmax = "10000",
STAR.Alignment.alignEndsType = "Local",
STAR.Alignment.winAnchorMultimapNmax = "50",
STAR.Alignment.winBinNbits = "16",
STAR.Alignment.winAnchorDistNbins = "9",
STAR.Alignment.winFlankNbins = "4",
Rsamtools.Bam.run = TRUE,
Samtools.Bam.num.parallel.threads = "1",
Rsamtools.nCores = "1",
StringTie.Assemble.run = TRUE,
Stringtie.Assembly.num.parallel.threads = "1",
Stringtie.Assembly.f = "0.1",
Stringtie.Assembly.m = "200",
Stringtie.Assembly.c = "2.5",
Stringtie.Assembly.g = "50",
Stringtie.Assembly.M = "0.95",
StringTie.Merge.Trans.run = TRUE,
Stringtie.Merge.num.parallel.threads = "1",
Gffcompare.Ref.Sample.run = TRUE,
StringTie.Ballgown.run = TRUE,
Stringtie.2.Ballgown.num.parallel.threads = "1",
PreDECountTable.run = TRUE,
check.s4.print = TRUE) {
CheckOperatingSystem(FALSE)
if (SAMtools.or.Rsamtools != "Rsamtools" &
SAMtools.or.Rsamtools != "SAMtools") {
stop("'SAMtools.or.Rsamtools' must be 'Rsamtools' or 'SAMtools'!!")
}
# If `which.trigger` is OUTSIDE, then directory must be built
# If `which.trigger` is INSIDE, then directory must not be
# built here(will created in CMD)
if (isS4(RNASeqRParam) &
which.trigger == "OUTSIDE" &
is.na(INSIDE.path.prefix)) {
# This is an external call!!
# Check the S4 object(user input)
} else if (RNASeqRParam == "INSIDE" &
which.trigger == "INSIDE" &
!is.na(INSIDE.path.prefix)) {
# This is an internal call!!
# Load the S4 object that saved in CMD process
RNASeqRParam <- readRDS(paste0(INSIDE.path.prefix,
"gene_data/RNASeqRParam.rds"))
}
which.s4.object <- CheckS4Object_All(RNASeqRParam, check.s4.print)
# To find 'HISAT2', 'StringTie' and 'Gffcompare'
path.prefix <- "@"(RNASeqRParam, path.prefix)
input.path.prefix <- "@"(RNASeqRParam, input.path.prefix)
genome.name <- "@"(RNASeqRParam, genome.name)
sample.pattern <- "@"(RNASeqRParam, sample.pattern)
independent.variable <- "@"(RNASeqRParam, independent.variable)
case.group <- "@"(RNASeqRParam, case.group)
control.group <- "@"(RNASeqRParam, control.group)
python.variable <- "@"(RNASeqRParam, python.variable)
python.variable.answer <- python.variable$check.answer
python.variable.version <- python.variable$python.version
python.2to3 <- "@"(RNASeqRParam, python.2to3)
fastq.gz.type <- "@"(RNASeqRParam, fastq.gz.type)
ExportPath(path.prefix)
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
if (which.s4.object == "RNASeqRParam") {
indices.optional <- "@"(RNASeqRParam, indices.optional)
PreRNASeqReadProcess(path.prefix, genome.name, sample.pattern)
# Check alignemnt selection first !
if (isTRUE(Hisat2.Alignment.run) && isTRUE(STAR.Alignment.run)) {
stop("Hisat2 and STAR can not run at the same time !")
} else if (isTRUE(Hisat2.Alignment.run) && !isTRUE(STAR.Alignment.run)) {
message("Hisat2 is selected as aligner in the pipeline !")
} else if (!isTRUE(Hisat2.Alignment.run) && isTRUE(STAR.Alignment.run)) {
message("STAR is selected as aligner in the pipeline !")
}
if (check.results$ht2.files.number.df == 0 &&
!indices.optional & Hisat2.Index.run) {
# Parameters: 11
CreateHisat2Index(path.prefix,
genome.name,
sample.pattern,
splice.site.info = TRUE,
exon.info = TRUE,
Hisat2.Index.num.parallel.threads,
Hisat2.Index.large.index,
Hisat2.Index.local.ftab.chars,
Hisat2.Index.local.off.rate,
Hisat2.Index.ftab.chars,
Hisat2.Index.off.rate)
}
if (Hisat2.Alignment.run) {
# Parameters: 43
Hisat2AlignmentDefault(path.prefix,
fastq.gz.type,
genome.name,
sample.pattern,
independent.variable,
case.group,
control.group,
Hisat2.Alignment.num.parallel.threads,
Hisat2.Alignment.skip,
Hisat2.Alignment.trim5,
Hisat2.Alignment.trim3,
Hisat2.Alignment.n.ceil.1.function.type,
Hisat2.Alignment.n.ceil.2.constant.term,
Hisat2.Alignment.n.ceil.3.coefficient,
Hisat2.Alignment.mp.MX,
Hisat2.Alignment.mp.MN,
Hisat2.Alignment.sp.MX,
Hisat2.Alignment.sp.MN,
Hisat2.Alignment.np,
Hisat2.Alignment.rdg.1,
Hisat2.Alignment.rdg.2,
Hisat2.Alignment.rfg.1,
Hisat2.Alignment.rfg.2,
Hisat2.Alignment.score.min.1.function.type,
Hisat2.Alignment.score.min.2.constant.term,
Hisat2.Alignment.score.min.3.coefficient,
Hisat2.Alignment.pen.cansplice,
Hisat2.Alignment.penc.noncansplice,
Hisat2.Alignment.pen.canintronlen.1.function.type,
Hisat2.Alignment.pen.canintronlen.2.constant.term,
Hisat2.Alignment.pen.canintronlen.3.coefficient,
Hisat2.Alignment.pen.noncanintronlen.1.function.type,
Hisat2.Alignment.pen.noncanintronlen.2.constant.term,
Hisat2.Alignment.pen.noncanintronlen.3.coefficient,
Hisat2.Alignment.min.intronlen,
Hisat2.Alignment.max.intronlen,
Hisat2.Alignment.rna.strandness,
Hisat2.Alignment.k,
Hisat2.Alignment.max.seeds,
Hisat2.Alignment.secondary,
Hisat2.Alignment.minins,
Hisat2.Alignment.maxins,
Hisat2.Alignment.seed)
}
if (STAR.Alignment.run) {
# Parameters: 8
CreateSTARIndex(path.prefix,
genome.name,
sample.pattern,
STAR.Index.num.parallel.threads,
STAR.Index.sjdbOverhang.Read.length,
STAR.Index.genomeSAindexNbases,
STAR.Index.genomeChrBinNbits,
STAR.Index.genomeSAsparseD)
# Parameters: 53
STARAlignmentDefault(path.prefix,
fastq.gz.type,
genome.name,
sample.pattern,
STAR.Alignment.num.parallel.threads,
STAR.Alignment.genomeLoad,
STAR.Alignment.readMapNumber,
STAR.Alignment.clip3pNbases,
STAR.Alignment.clip5pNbases,
STAR.Alignment.clip3pAdapterSeq,
STAR.Alignment.clip3pAdapterMMp,
STAR.Alignment.clip3pAfterAdapterNbases,
STAR.Alignment.limitGenomeGenerateRAM,
STAR.Alignment.limitIObufferSize,
STAR.Alignment.limitOutSAMoneReadBytes,
STAR.Alignment.limitOutSJoneRead,
STAR.Alignment.limitOutSJcollapsed,
STAR.Alignment.limitBAMsortRAM,
STAR.Alignment.outReadsUnmapped,
STAR.Alignment.outQSconversionAdd,
STAR.Alignment.outSAMprimaryFlag,
STAR.Alignment.outSAMmapqUnique,
STAR.Alignment.scoreGap,
STAR.Alignment.scoreGapNoncan,
STAR.Alignment.scoreGapGCAG,
STAR.Alignment.scoreGapATAC,
STAR.Alignment.scoreGenomicLengthLog2scale,
STAR.Alignment.scoreDelOpen,
STAR.Alignment.scoreDelBase,
STAR.Alignment.scoreInsOpen,
STAR.Alignment.scoreInsBase,
STAR.Alignment.scoreStitchSJshift,
STAR.Alignment.seedSearchStartLmax,
STAR.Alignment.seedSearchStartLmaxOverLread,
STAR.Alignment.seedSearchLmax,
STAR.Alignment.seedMultimapNmax,
STAR.Alignment.seedPerReadNmax,
STAR.Alignment.seedPerWindowNmax,
STAR.Alignment.seedNoneLociPerWindow,
STAR.Alignment.alignIntronMin,
STAR.Alignment.alignIntronMax,
STAR.Alignment.alignMatesGapMax,
STAR.Alignment.alignSJoverhangMin,
STAR.Alignment.alignSJDBoverhangMin,
STAR.Alignment.alignSplicedMateMapLmin,
STAR.Alignment.alignSplicedMateMapLminOverLmate,
STAR.Alignment.alignWindowsPerReadNmax,
STAR.Alignment.alignTranscriptsPerWindowNmax,
STAR.Alignment.alignTranscriptsPerReadNmax,
STAR.Alignment.alignEndsType,
STAR.Alignment.winAnchorMultimapNmax,
STAR.Alignment.winBinNbits,
STAR.Alignment.winAnchorDistNbins,
STAR.Alignment.winFlankNbins)
}
if (Rsamtools.Bam.run) {
# Parameters: 6
RSamtoolsToBam(SAMtools.or.Rsamtools,
Samtools.Bam.num.parallel.threads,
path.prefix,
genome.name,
sample.pattern,
Rsamtools.nCores)
}
} else if (which.s4.object == "RNASeqRParam_Sam") {
PreRNASeqReadProcess_Sam(path.prefix, genome.name, sample.pattern)
if (Rsamtools.Bam.run) {
# Parameters: 6
RSamtoolsToBam(SAMtools.or.Rsamtools,
Samtools.Bam.num.parallel.threads,
path.prefix,
genome.name,
sample.pattern,
Rsamtools.nCores)
}
} else if (which.s4.object == "RNASeqRParam_Bam") {
PreRNASeqReadProcess_Bam(path.prefix, genome.name, sample.pattern)
}
if (StringTie.Assemble.run) {
# Parameters: 9
StringTieAssemble(path.prefix,
genome.name,
sample.pattern,
Stringtie.Assembly.num.parallel.threads,
Stringtie.Assembly.f,
Stringtie.Assembly.m,
Stringtie.Assembly.c,
Stringtie.Assembly.g,
Stringtie.Assembly.M)
}
if (StringTie.Merge.Trans.run) {
# Parameters: 4
StringTieMergeTrans(path.prefix,
genome.name,
sample.pattern,
Stringtie.Merge.num.parallel.threads)
}
if (Gffcompare.Ref.Sample.run) {
# Parameters: 3
GffcompareRefSample(path.prefix,
genome.name,
sample.pattern)
}
if (StringTie.Ballgown.run) {
# Parameters: 4
StringTieToBallgown(path.prefix,
genome.name,
sample.pattern,
Stringtie.2.Ballgown.num.parallel.threads)
}
finals <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=TRUE)
if (PreDECountTable.run &
((python.variable.answer & python.variable.version == 2) |
python.variable.answer & python.variable.version == 3 & python.2to3)) {
# Parameters: 6
PreDECountTable(path.prefix,
sample.pattern,
python.variable.answer,
python.variable.version,
python.2to3,
print=TRUE)
}
if (which.s4.object == "RNASeqRParam") {
PostRNASeqReadProcess(path.prefix,
genome.name,
sample.pattern)
} else if (which.s4.object == "RNASeqRParam_Sam") {
PostRNASeqReadProcess_Sam(path.prefix,
genome.name,
sample.pattern)
} else if (which.s4.object == "RNASeqRParam_Bam") {
PostRNASeqReadProcess_Bam(path.prefix,
genome.name,
sample.pattern)
}
}
PreRNASeqReadProcess <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment pre-check ...\n")
phenodata.csv <- file.exists(paste0(path.prefix, "gene_data/phenodata.csv"))
ref.gtf <- file.exists(paste0(path.prefix,
"gene_data/ref_genes/", genome.name, ".gtf"))
ref.fa <- file.exists(paste0(path.prefix,
"gene_data/ref_genome/", genome.name, ".fa"))
raw.fastq <- list.files(path = paste0(path.prefix, 'gene_data/raw_fastq.gz/'),
pattern = sample.pattern,
all.files = FALSE,
full.names = FALSE,
recursive = FALSE,
ignore.case = FALSE)
check.tool.result <- CheckToolAll(path.prefix)
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
check.progress.results.bool <- check.results$gtf.file.logic.df &&
check.results$fa.file.logic.df &&
(check.results$fastq.gz.files.number.df != 0)
validity <- phenodata.csv && ref.gtf && ref.fa && check.tool.result &&
(length(raw.fastq) != 0) && check.progress.results.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() environment ERROR")
}
message("(\u2714) : RNASeqReadProcess() pre-check is valid\n\n")
}
PreRNASeqReadProcess_Sam <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment pre-check ...\n")
phenodata.csv <- file.exists(paste0(path.prefix, "gene_data/phenodata.csv"))
ref.gtf <- file.exists(paste0(path.prefix,
"gene_data/ref_genes/", genome.name, ".gtf"))
raw.sam <- list.files(path = paste0(path.prefix, 'gene_data/raw_sam/'),
pattern = sample.pattern,
all.files = FALSE,
full.names = FALSE,
recursive = FALSE,
ignore.case = FALSE)
check.tool.result <- CheckTool_Sam_Bam(path.prefix)
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
check.progress.results.bool <- check.results$gtf.file.logic.df &&
(check.results$sam.files.number.df != 0)
validity <- phenodata.csv && ref.gtf && check.tool.result &&
(length(raw.sam) != 0) && check.progress.results.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() environment ERROR")
}
message("(\u2714) : RNASeqReadProcess() pre-check is valid\n\n")
}
PreRNASeqReadProcess_Bam <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment pre-check ...\n")
phenodata.csv <- file.exists(paste0(path.prefix, "gene_data/phenodata.csv"))
ref.gtf <- file.exists(paste0(path.prefix,
"gene_data/ref_genes/", genome.name, ".gtf"))
raw.bam <- list.files(path = paste0(path.prefix, 'gene_data/raw_bam/'),
pattern = sample.pattern,
all.files = FALSE,
full.names = FALSE,
recursive = FALSE,
ignore.case = FALSE)
check.tool.result <- CheckTool_Sam_Bam(path.prefix)
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
check.progress.results.bool <- check.results$gtf.file.logic.df &&
(check.results$bam.files.number.df != 0)
validity <- phenodata.csv && ref.gtf && check.tool.result &&
(length(raw.bam) != 0) && check.progress.results.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() environment ERROR")
}
message("(\u2714) : RNASeqReadProcess() pre-check is valid\n\n")
}
PostRNASeqReadProcess <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment post-check ...\n")
# Still need to add condition
gene_abundance <- dir.exists(paste0(path.prefix, "gene_data/gene_abundance/"))
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
ht2.bool <- (check.results$ht2.files.number.df) != 0
sam.bool <- (check.results$sam.files.number.df) != 0
bam.bool <- (check.results$bam.files.number.df) != 0
gtf.bool <- (check.results$gtf.files.number.df) != 0
merged.bool <- check.results$stringtie_merged.gtf.file.df
gffcompare.bool <- (check.results$gffcompare.related.dirs.number.df) != 0
ballgown.bool <- (check.results$ballgown.dirs.number.df) != 0
validity <- gene_abundance && ht2.bool && sam.bool && bam.bool && gtf.bool &&
merged.bool && gffcompare.bool && ballgown.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() post-check ERROR")
}
message("(\u2714) : RNASeqReadProcess() post-check is valid\n\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605 Success!! \u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
}
PostRNASeqReadProcess_Sam <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment post-check ...\n")
# Still need to add condition
gene_abundance <- dir.exists(paste0(path.prefix, "gene_data/gene_abundance/"))
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
sam.bool <- (check.results$sam.files.number.df) != 0
bam.bool <- (check.results$bam.files.number.df) != 0
gtf.bool <- (check.results$gtf.files.number.df) != 0
merged.bool <- check.results$stringtie_merged.gtf.file.df
gffcompare.bool <- (check.results$gffcompare.related.dirs.number.df) != 0
ballgown.bool <- (check.results$ballgown.dirs.number.df) != 0
validity <- gene_abundance && sam.bool && bam.bool && gtf.bool &&
merged.bool && gffcompare.bool && ballgown.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() post-check ERROR")
}
message("(\u2714) : RNASeqReadProcess() post-check is valid\n\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605 Success!! \u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
}
PostRNASeqReadProcess_Bam <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment post-check ...\n")
# Still need to add condition
gene_abundance <- dir.exists(paste0(path.prefix, "gene_data/gene_abundance/"))
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
bam.bool <- (check.results$bam.files.number.df) != 0
gtf.bool <- (check.results$gtf.files.number.df) != 0
merged.bool <- check.results$stringtie_merged.gtf.file.df
gffcompare.bool <- (check.results$gffcompare.related.dirs.number.df) != 0
ballgown.bool <- (check.results$ballgown.dirs.number.df) != 0
validity <- gene_abundance && bam.bool && gtf.bool &&
merged.bool && gffcompare.bool && ballgown.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() post-check ERROR")
}
message("(\u2714) : RNASeqReadProcess() post-check is valid\n\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605 Success!! \u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
}
Kuanhao-Chao/RNASeqR documentation built on May 12, 2022, 8:15 a.m.
R Package Documentation
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Defines functions PostRNASeqReadProcess_Bam PostRNASeqReadProcess_Sam PostRNASeqReadProcess PreRNASeqReadProcess_Bam PreRNASeqReadProcess_Sam PreRNASeqReadProcess RNASeqReadProcess RNASeqReadProcess_CMD
Documented in RNASeqReadProcess RNASeqReadProcess_CMD
#' @title RNASeqReadProcess_CMD
#'
#' @description
#' Process raw reads for RNA-Seq workflow in background. \cr
#' This function do 5 things : \cr
#' \enumerate{
#' \item 'Hisat2' : aligns raw reads to reference genome.
#' If \code{indices.optional} in \code{RNASeqRParam} is
#' \code{FALSE}, Hisat2 indices will be created.\cr
#' \item 'Rsamtools': converts '.sam' files to '.bam' files.\cr
#' \item 'Stringtie': assembles alignments into transcript.\cr
#' \item 'Gffcompare': examines how transcripts compare with the
#' reference annotation. \cr
#' \item 'Stringtie': creates input files for ballgown, edgeR and DESeq2.\cr
#' \item raw reads count: create raw reads count for DESeq2 and edgeR \cr
#' }
#' Before running this function, \code{RNASeqEnvironmentSet_CMD()} or
#' \code{RNASeqEnvironmentSet()} must be executed successfully. \cr
#' If you want to process raw reads for the following RNA-Seq workflow
#' in R shell, please see \code{RNASeqReadProcess()} function.\cr
#'
#' @param RNASeqRParam S4 object instance of experiment-related
#' parameters
#' @param SAMtools.or.Rsamtools Default value is \code{Rsamtools}. User can set
#' to \code{SAMtools} to use command-line-based 'samtools' instead.
#' @param Hisat2.Index.run Whether to run 'HISAT2 index' step in this function
#' step. Default value is \code{TRUE}. Set \code{FALSE} to skip
#' 'HISAT2 index' step.
#' @param Hisat2.Index.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Hisat2 index step. The default is \code{"1"}
#' @param Hisat2.Index.large.index Hisat2 index terminal '--large-index' option.
#' Default value is \code{FALSE}
#' @param Hisat2.Index.local.ftab.chars Hisat2 index terminal '-t/--ftabchars'
#' option. Default value is \code{"6"}
#' @param Hisat2.Index.local.off.rate Hisat2 index terminal '--localoffrate'
#' option. Default value is \code{"3"}
#' @param Hisat2.Index.ftab.chars Hisat2 index terminal '--localftabchars'
#' option. Default value is \code{"10"}
#' @param Hisat2.Index.off.rate Hisat2 index terminal '--offrate' option.
#' Default value is \code{"4"}
#' @param Hisat2.Alignment.run Whether to run 'HISAT2 alignment' step in this
#' function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'HISAT2 alignment' step.
#' @param Hisat2.Alignment.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Hisat2 alignment step. The default is \code{"1"}
#' @param Hisat2.Alignment.skip Hisat2 alignment terminal '-s/--skip' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.trim5 Hisat2 alignment terminal '-5/--trim5' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.trim3 Hisat2 alignment terminal '-3/--trim3' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.n.ceil.1.function.type Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"L"}
#' @param Hisat2.Alignment.n.ceil.2.constant.term Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"0"}
#' @param Hisat2.Alignment.n.ceil.3.coefficient Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"0.15"}
#' @param Hisat2.Alignment.mp.MX Hisat2 alignment terminal '--mp MX' option.
#' Default value is \code{"6"}
#' @param Hisat2.Alignment.mp.MN Hisat2 alignment terminal '--mp MN' option.
#' Default value is \code{"2"}
#' @param Hisat2.Alignment.sp.MX Hisat2 alignment terminal '--sp MX' option.
#' Default value is \code{"2"}
#' @param Hisat2.Alignment.sp.MN Hisat2 alignment terminal '--sp MN' option.
#' Default value is \code{"1"}
#' @param Hisat2.Alignment.np Hisat2 alignment terminal '--np' option.
#' Default value is \code{"1"}
#' @param Hisat2.Alignment.rdg.1 Hisat2 alignment terminal '--rdg' first option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.rdg.2 Hisat2 alignment terminal '--rdg' first option.
#' Default value is \code{"3"}
#' @param Hisat2.Alignment.rfg.1 Hisat2 alignment terminal '--rfg' first option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.rfg.2 Hisat2 alignment terminal '--rfg' first option.
#' Default value is \code{"3"}
#' @param Hisat2.Alignment.score.min.1.function.type Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"L"}
#' @param Hisat2.Alignment.score.min.2.constant.term Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"0"}
#' @param Hisat2.Alignment.score.min.3.coefficient Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"-0.2"}
#' @param Hisat2.Alignment.pen.cansplice Hisat2 alignment terminal
#' '--pen-cansplice' first option. Default value is \code{"-0"}
#' @param Hisat2.Alignment.penc.noncansplice Hisat2 alignment terminal
#' '--pen-noncansplice' option. Default value is \code{"12"}
#' @param Hisat2.Alignment.pen.canintronlen.1.function.type Hisat2 alignment
#' terminal '--pen-canintronlen' first option. Default value is \code{"G"}
#' @param Hisat2.Alignment.pen.canintronlen.2.constant.term Hisat2 alignment
#' terminal '--pen-canintronlen' second option. Default value is \code{"-8"}
#' @param Hisat2.Alignment.pen.canintronlen.3.coefficient Hisat2 alignment
#' terminal '--pen-canintronlen' third option. Default value is \code{"1"}
#' @param Hisat2.Alignment.pen.noncanintronlen.1.function.type Hisat2 alignment
#' terminal '--pen-noncanintronlen' first option. Default value is \code{"G"}
#' @param Hisat2.Alignment.pen.noncanintronlen.2.constant.term Hisat2 alignment
#' terminal '--pen-noncanintronlen' second option. Default value is \code{"-8"}
#' @param Hisat2.Alignment.pen.noncanintronlen.3.coefficient Hisat2 alignment
#' terminal '--pen-noncanintronlen' third option. Default value is \code{"1"}
#' @param Hisat2.Alignment.min.intronlen Hisat2 alignment terminal
#' '--min-intronlen' option. Default value is \code{"20"}
#' @param Hisat2.Alignment.max.intronlen Hisat2 alignment terminal '--max-intronlen'
#' option. Default value is \code{"20"}
#' @param Hisat2.Alignment.rna.strandness Hisat2 alignment terminal '--rna-strandness'
#' option. Default value is \code{"None"}
#' @param Hisat2.Alignment.k Hisat2 alignment terminal '-k' option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.max.seeds Hisat2 alignment terminal '--max-seeds' option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.secondary Hisat2 alignment terminal '--secondary' option.
#' Default value is \code{"FALSE"}
#' @param Hisat2.Alignment.minins Hisat2 alignment terminal '-I/--minins' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.maxins Hisat2 alignment terminal '-X/--maxins' option.
#' Default value is \code{"500"}
#' @param Hisat2.Alignment.seed Hisat2 alignment terminal '-X/--maxins' option.
#' Default value is \code{"0"}
#' @param STAR.Index.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for STAR index step. The default is \code{"1"}
#' @param STAR.Index.sjdbOverhang.Read.length STAR index terminal
#' '--sjdbOverhang' option. Default value is \code{"100"}
#' @param STAR.Index.genomeSAindexNbases STAR index terminal
#' '--genomeSAindexNbases' option. Default value is \code{"14"}
#' @param STAR.Index.genomeChrBinNbits STAR index terminal
#' '--genomeChrBinNbits' option. Default value is \code{"18"}
#' @param STAR.Index.genomeSAsparseD STAR index terminal
#' '--genomeSAsparseD' option. Default value is \code{"1"}
#' @param STAR.Alignment.run Whether to run 'STAR index' step in this function
#' step. Default value is \code{FALSE}. Set \code{TRUE} to run STAR alignment step.
#' (need to set Hisat2.Index.run to \code{FALSE})
#' @param STAR.Alignment.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for STAR alignment step. The default is \code{"1"}
#' @param STAR.Alignment.genomeLoad STAR alignment terminal '--genomeLoad'
#' option. Default value is \code{"NoSharedMemory"}
#' @param STAR.Alignment.readMapNumber STAR alignment terminal '--readMapNumber'
#' option. Default value is \code{"-1"}
#' @param STAR.Alignment.clip3pNbases STAR alignment terminal '--clip3pNbases'
#' option. Default value is \code{"0"}
#' @param STAR.Alignment.clip5pNbases STAR alignment terminal '--clip5pNbases'
#' option. Default value is \code{"0"}
#' @param STAR.Alignment.clip3pAdapterSeq STAR alignment terminal '--clip3pAdapterSeq'
#' option. Default value is \code{"-"}
#' @param STAR.Alignment.clip3pAdapterMMp STAR alignment terminal '--clip3pAdapterMMp'
#' option. Default value is \code{"0.1"}
#' @param STAR.Alignment.clip3pAfterAdapterNbases STAR alignment terminal
#' '--clip3pAfterAdapterNbases' option. Default value is \code{"0"}
#' @param STAR.Alignment.limitGenomeGenerateRAM STAR alignment terminal
#' '--limitGenomeGenerateRAM' option. Default value is \code{"31000000000"}
#' @param STAR.Alignment.limitIObufferSize STAR alignment terminal
#' '--limitIObufferSize' option. Default value is \code{"150000000"}
#' @param STAR.Alignment.limitOutSAMoneReadBytes STAR alignment terminal
#' '--limitOutSAMoneReadBytes' option. Default value is \code{"100000"}
#' @param STAR.Alignment.limitOutSJoneRead STAR alignment terminal
#' '--limitOutSJoneRead' option. Default value is \code{"1000"}
#' @param STAR.Alignment.limitOutSJcollapsed STAR alignment terminal
#' '--limitOutSJcollapsed' option. Default value is \code{"1000000"}
#' @param STAR.Alignment.limitBAMsortRAM STAR alignment terminal
#' '--limitBAMsortRAM' option. Default value is \code{"0"}
#' @param STAR.Alignment.outReadsUnmapped STAR alignment terminal
#' '--outReadsUnmapped' option. Default value is \code{"None"}
#' @param STAR.Alignment.outQSconversionAdd STAR alignment terminal
#' '--outQSconversionAdd' option. Default value is \code{"0"}
#' @param STAR.Alignment.outSAMprimaryFlag STAR alignment terminal
#' '--outSAMprimaryFlag' option. Default value is \code{"OneBestScore"}
#' @param STAR.Alignment.outSAMmapqUnique STAR alignment terminal
#' '--outSAMmapqUnique' option. Default value is \code{"255"}
#' @param STAR.Alignment.scoreGap STAR alignment terminal
#' '--scoreGap' option. Default value is \code{"0"}
#' @param STAR.Alignment.scoreGapNoncan STAR alignment terminal
#' '--scoreGapNoncan' option. Default value is \code{"-8"}
#' @param STAR.Alignment.scoreGapGCAG STAR alignment terminal
#' '--scoreGapGCAG' option. Default value is \code{"-4"}
#' @param STAR.Alignment.scoreGapATAC STAR alignment terminal
#' '--scoreGapATAC' option. Default value is \code{"-8"}
#' @param STAR.Alignment.scoreGenomicLengthLog2scale STAR alignment terminal
#' '--scoreGenomicLengthLog2scale' option. Default value is \code{"-0.25"}
#' @param STAR.Alignment.scoreDelOpen STAR alignment terminal
#' '--scoreDelOpen' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreDelBase STAR alignment terminal
#' '--scoreDelBase' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreInsOpen STAR alignment terminal
#' '--scoreInsOpen' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreInsBase STAR alignment terminal
#' '--scoreInsBase' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreStitchSJshift STAR alignment terminal
#' '--scoreStitchSJshift' option. Default value is \code{"1"}
#' @param STAR.Alignment.seedSearchStartLmax STAR alignment terminal
#' '--scoreStitchSJshift' option. Default value is \code{"50"}
#' @param STAR.Alignment.seedSearchStartLmaxOverLread STAR alignment terminal
#' '--seedSearchStartLmaxOverLread' option. Default value is \code{"1.0"}
#' @param STAR.Alignment.seedSearchLmax STAR alignment terminal
#' '--seedSearchLmax' option. Default value is \code{"0"}
#' @param STAR.Alignment.seedMultimapNmax STAR alignment terminal
#' '--seedMultimapNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.seedPerReadNmax STAR alignment terminal
#' '--seedPerReadNmax' option. Default value is \code{"1000"}
#' @param STAR.Alignment.seedPerWindowNmax STAR alignment terminal
#' '--seedPerWindowNmax' option. Default value is \code{"50"}
#' @param STAR.Alignment.seedNoneLociPerWindow STAR alignment terminal
#' '--seedNoneLociPerWindow' option. Default value is \code{"10"}
#' @param STAR.Alignment.alignIntronMin STAR alignment terminal
#' '--alignIntronMin' option. Default value is \code{"21"}
#' @param STAR.Alignment.alignIntronMax STAR alignment terminal
#' '--alignIntronMax' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignMatesGapMax STAR alignment terminal
#' '--alignMatesGapMax' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignSJoverhangMin STAR alignment terminal
#' '--alignSJoverhangMin' option. Default value is \code{"5"}
#' @param STAR.Alignment.alignSJDBoverhangMin STAR alignment terminal
#' '--alignSJDBoverhangMin' option. Default value is \code{"3"}
#' @param STAR.Alignment.alignSplicedMateMapLmin STAR alignment terminal
#' '--alignSplicedMateMapLmin' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignSplicedMateMapLminOverLmate STAR alignment terminal
#' '--alignSplicedMateMapLminOverLmate' option. Default value is \code{"0.66"}
#' @param STAR.Alignment.alignWindowsPerReadNmax STAR alignment terminal
#' '--alignWindowsPerReadNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.alignTranscriptsPerWindowNmax STAR alignment terminal
#' '--alignTranscriptsPerWindowNmax' option. Default value is \code{"100"}
#' @param STAR.Alignment.alignTranscriptsPerReadNmax STAR alignment terminal
#' '--alignTranscriptsPerReadNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.alignEndsType STAR alignment terminal
#' '--alignEndsType' option. Default value is \code{"Local"}
#' @param STAR.Alignment.winAnchorMultimapNmax STAR alignment terminal
#' '--winAnchorMultimapNmax' option. Default value is \code{"50"}
#' @param STAR.Alignment.winBinNbits STAR alignment terminal
#' '--winBinNbits' option. Default value is \code{"16"}
#' @param STAR.Alignment.winAnchorDistNbins STAR alignment terminal
#' '--winAnchorDistNbins' option. Default value is \code{"9"}
#' @param STAR.Alignment.winFlankNbins STAR alignment terminal
#' '--winFlankNbins' option. Default value is \code{"4"}
#' @param Rsamtools.Bam.run Whether to run 'Rsamtools SAM to BAM' step in this
#' function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'Rsamtools SAM to BAM' step.
#' @param Samtools.Bam.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Samtools sam to bam step. The default is \code{"1"}
#' @param Rsamtools.nCores The number of cores to use when running
#' 'Rsamtools' step. Default value is \code{1}
#' @param StringTie.Assemble.run Whether to run 'StringTie assembly' step in
#' this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie assembly' step.
#' @param Stringtie.Assembly.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie assembly. The default is \code{"1"}
#' @param Stringtie.Assembly.f Stringtie assembly terminal
#' '-f' option. Default value is \code{"0.1"}
#' @param Stringtie.Assembly.m Stringtie assembly terminal
#' '-m' option. Default value is \code{"200"}
#' @param Stringtie.Assembly.c Stringtie assembly terminal
#' '-c' option. Default value is \code{"2.5"}
#' @param Stringtie.Assembly.g Stringtie assembly terminal
#' '-g' option. Default value is \code{"50"}
#' @param Stringtie.Assembly.M Stringtie assembly terminal
#' '-M' option. Default value is \code{"0.95"}
#' @param StringTie.Merge.Trans.run Whether to run 'StringTie GTF merging' step
#' in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie GTF merging' step.
#' @param Stringtie.Merge.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie merge step. The default is \code{"1"}
#' @param Gffcompare.Ref.Sample.run Whether to run 'Gffcompare comparison' step
#' in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'Gffcompare comparison' step.
#' @param StringTie.Ballgown.run Whether to run 'StringTie ballgown creation'
#' step in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie ballgown creation' step.
#' @param Stringtie.2.Ballgown.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie to ballgown step. The default is \code{"1"}
#' @param PreDECountTable.run Whether to run 'gene raw reads count creation'
#' step in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'gene raw reads count creation' step.
#' @param run Default value is \code{TRUE}. If \code{TRUE},
#' 'Rscript/Environment_Set.R' will be created and executed.
#' The output log will be stored in 'Rscript_out/Environment_Set.Rout'.
#' If \code{False}, 'Rscript/Environment_Set.R' will be
#' created without executed.
#' @param check.s4.print Default \code{TRUE}. If \code{TRUE},
#' the result of checking \code{RNASeqRParam}
#' will be reported in 'Rscript_out/Environment_Set.Rout'. If \code{FALSE},
#' the result of checking \code{RNASeqRParam} will not be in
#' 'Rscript_out/Environment_Set.Rout'.
#'
#' @return None
#' @export
#' @author Kuan-Hao Chao
#' @examples
#' data(yeast)
#' \dontrun{
#' ## Before run this function, make sure \code{RNASeqEnvironmentSet_CMD()}
#' ## (or\code{RNASeqEnvironmentSet()}) is executed successfully.
#' RNASeqReadProcess_CMD(RNASeqRParam = yeast,
#' num.parallel.threads = 10)}
#'
# Parameters: 119
RNASeqReadProcess_CMD <- function(RNASeqRParam,
SAMtools.or.Rsamtools = "Rsamtools",
Hisat2.Index.run = TRUE,
Hisat2.Index.num.parallel.threads = "1",
Hisat2.Index.large.index = FALSE,
Hisat2.Index.local.ftab.chars = "6",
Hisat2.Index.local.off.rate = "3",
Hisat2.Index.ftab.chars = "10",
Hisat2.Index.off.rate = "4",
Hisat2.Alignment.run = TRUE,
Hisat2.Alignment.num.parallel.threads = "1",
Hisat2.Alignment.skip = "0",
Hisat2.Alignment.trim5 = "0",
Hisat2.Alignment.trim3 = "0",
Hisat2.Alignment.n.ceil.1.function.type = "L",
Hisat2.Alignment.n.ceil.2.constant.term = "0",
Hisat2.Alignment.n.ceil.3.coefficient = "0.15",
Hisat2.Alignment.mp.MX = "6",
Hisat2.Alignment.mp.MN = "2",
Hisat2.Alignment.sp.MX = "2",
Hisat2.Alignment.sp.MN = "1",
Hisat2.Alignment.np = "1",
Hisat2.Alignment.rdg.1 = "5",
Hisat2.Alignment.rdg.2 = "3",
Hisat2.Alignment.rfg.1 = "5",
Hisat2.Alignment.rfg.2 = "3",
Hisat2.Alignment.score.min.1.function.type = "L",
Hisat2.Alignment.score.min.2.constant.term = "0",
Hisat2.Alignment.score.min.3.coefficient = "-0.2",
Hisat2.Alignment.pen.cansplice = "0",
Hisat2.Alignment.penc.noncansplice = "12",
Hisat2.Alignment.pen.canintronlen.1.function.type = "G",
Hisat2.Alignment.pen.canintronlen.2.constant.term = "-8",
Hisat2.Alignment.pen.canintronlen.3.coefficient = "1",
Hisat2.Alignment.pen.noncanintronlen.1.function.type = "G",
Hisat2.Alignment.pen.noncanintronlen.2.constant.term = "-8",
Hisat2.Alignment.pen.noncanintronlen.3.coefficient = "1",
Hisat2.Alignment.min.intronlen = "20",
Hisat2.Alignment.max.intronlen = "500000",
Hisat2.Alignment.rna.strandness = "None",
Hisat2.Alignment.k = "5",
Hisat2.Alignment.max.seeds = "5",
Hisat2.Alignment.secondary = FALSE,
Hisat2.Alignment.minins = "0",
Hisat2.Alignment.maxins = "500",
Hisat2.Alignment.seed = "0",
STAR.Index.num.parallel.threads = "1",
STAR.Index.sjdbOverhang.Read.length = "100",
STAR.Index.genomeSAindexNbases = "14",
STAR.Index.genomeChrBinNbits = "18",
STAR.Index.genomeSAsparseD = "1",
STAR.Alignment.run = FALSE,
STAR.Alignment.num.parallel.threads = "1",
STAR.Alignment.genomeLoad = "NoSharedMemory",
STAR.Alignment.readMapNumber = "-1",
STAR.Alignment.clip3pNbases = "0",
STAR.Alignment.clip5pNbases = "0",
STAR.Alignment.clip3pAdapterSeq = "-",
STAR.Alignment.clip3pAdapterMMp = "0.1",
STAR.Alignment.clip3pAfterAdapterNbases = "0",
STAR.Alignment.limitGenomeGenerateRAM = "31000000000",
STAR.Alignment.limitIObufferSize = "150000000",
STAR.Alignment.limitOutSAMoneReadBytes = "100000",
STAR.Alignment.limitOutSJoneRead = "1000",
STAR.Alignment.limitOutSJcollapsed = "1000000",
STAR.Alignment.limitBAMsortRAM = "0",
STAR.Alignment.outReadsUnmapped = "None",
STAR.Alignment.outQSconversionAdd = "0",
STAR.Alignment.outSAMprimaryFlag = "OneBestScore",
STAR.Alignment.outSAMmapqUnique = "255",
STAR.Alignment.scoreGap = "0",
STAR.Alignment.scoreGapNoncan = "-8",
STAR.Alignment.scoreGapGCAG = "-4",
STAR.Alignment.scoreGapATAC = "-8",
STAR.Alignment.scoreGenomicLengthLog2scale = "-0.25",
STAR.Alignment.scoreDelOpen = "-2",
STAR.Alignment.scoreDelBase = "-2",
STAR.Alignment.scoreInsOpen = "-2",
STAR.Alignment.scoreInsBase = "-2",
STAR.Alignment.scoreStitchSJshift = "1",
STAR.Alignment.seedSearchStartLmax = "50",
STAR.Alignment.seedSearchStartLmaxOverLread = "1.0",
STAR.Alignment.seedSearchLmax = "0",
STAR.Alignment.seedMultimapNmax = "10000",
STAR.Alignment.seedPerReadNmax = "1000",
STAR.Alignment.seedPerWindowNmax = "50",
STAR.Alignment.seedNoneLociPerWindow = "10",
STAR.Alignment.alignIntronMin = "21",
STAR.Alignment.alignIntronMax = "0",
STAR.Alignment.alignMatesGapMax = "0",
STAR.Alignment.alignSJoverhangMin = "5",
STAR.Alignment.alignSJDBoverhangMin = "3",
STAR.Alignment.alignSplicedMateMapLmin = "0",
STAR.Alignment.alignSplicedMateMapLminOverLmate = "0.66",
STAR.Alignment.alignWindowsPerReadNmax = "10000",
STAR.Alignment.alignTranscriptsPerWindowNmax = "100",
STAR.Alignment.alignTranscriptsPerReadNmax = "10000",
STAR.Alignment.alignEndsType = "Local",
STAR.Alignment.winAnchorMultimapNmax = "50",
STAR.Alignment.winBinNbits = "16",
STAR.Alignment.winAnchorDistNbins = "9",
STAR.Alignment.winFlankNbins = "4",
Rsamtools.Bam.run = TRUE,
Samtools.Bam.num.parallel.threads = "1",
Rsamtools.nCores = "1",
StringTie.Assemble.run = TRUE,
Stringtie.Assembly.num.parallel.threads = "1",
Stringtie.Assembly.f = "0.1",
Stringtie.Assembly.m = "200",
Stringtie.Assembly.c = "2.5",
Stringtie.Assembly.g = "50",
Stringtie.Assembly.M = "0.95",
StringTie.Merge.Trans.run = TRUE,
Stringtie.Merge.num.parallel.threads = "1",
Gffcompare.Ref.Sample.run = TRUE,
StringTie.Ballgown.run = TRUE,
Stringtie.2.Ballgown.num.parallel.threads = "1",
PreDECountTable.run = TRUE,
run = TRUE,
check.s4.print = TRUE) {
which.s4.object <- CheckS4Object_All(RNASeqRParam, check.s4.print)
CheckOperatingSystem(FALSE)
path.prefix <- "@"(RNASeqRParam, path.prefix)
INSIDE.path.prefix <- "@"(RNASeqRParam, path.prefix)
saveRDS(RNASeqRParam,
file = paste0(INSIDE.path.prefix,
"gene_data/RNASeqRParam.rds"))
fileConn<-file(paste0(path.prefix, "Rscript/Read_Process.R"))
first <- "library(RNASeqR)"
if (which.s4.object == "RNASeqRParam") {
} else if (which.s4.object == "RNASeqRParam_Sam") {
Hisat2.Index.run = FALSE
Hisat2.Alignment.run = FALSE
STAR.Alignment.run = FALSE
} else if (which.s4.object == "RNASeqRParam_Bam") {
Hisat2.Index.run = FALSE
Hisat2.Alignment.run = FALSE
STAR.Alignment.run = FALSE
Rsamtools.Bam.run = FALSE
}
second <- paste0("RNASeqReadProcess(RNASeqRParam = 'INSIDE'",
", which.trigger = 'INSIDE'",
", INSIDE.path.prefix = '", INSIDE.path.prefix,
"', SAMtools.or.Rsamtools ='", SAMtools.or.Rsamtools,
"', Hisat2.Index.run =", Hisat2.Index.run,
", Hisat2.Index.num.parallel.threads = '", Hisat2.Index.num.parallel.threads,
"', Hisat2.Index.large.index = ", Hisat2.Index.large.index,
", Hisat2.Index.local.ftab.chars = '", Hisat2.Index.local.ftab.chars,
"', Hisat2.Index.local.off.rate = '", Hisat2.Index.local.off.rate,
"', Hisat2.Index.ftab.chars = '", Hisat2.Index.ftab.chars,
"', Hisat2.Index.off.rate = '", Hisat2.Index.off.rate,
"', Hisat2.Alignment.run = ", Hisat2.Alignment.run,
", Hisat2.Alignment.num.parallel.threads = '", Hisat2.Alignment.num.parallel.threads,
"', Hisat2.Alignment.skip = '", Hisat2.Alignment.skip,
"', Hisat2.Alignment.trim5 = '", Hisat2.Alignment.trim5,
"', Hisat2.Alignment.trim3 = '", Hisat2.Alignment.trim3,
"', Hisat2.Alignment.n.ceil.1.function.type = '", Hisat2.Alignment.n.ceil.1.function.type,
"', Hisat2.Alignment.n.ceil.2.constant.term = '", Hisat2.Alignment.n.ceil.2.constant.term,
"', Hisat2.Alignment.n.ceil.3.coefficient = '", Hisat2.Alignment.n.ceil.3.coefficient,
"', Hisat2.Alignment.mp.MX = '", Hisat2.Alignment.mp.MX,
"', Hisat2.Alignment.mp.MN = '", Hisat2.Alignment.mp.MN,
"', Hisat2.Alignment.sp.MX = '", Hisat2.Alignment.sp.MX,
"', Hisat2.Alignment.sp.MN = '", Hisat2.Alignment.sp.MN,
"', Hisat2.Alignment.np = '", Hisat2.Alignment.np,
"', Hisat2.Alignment.rdg.1 = '", Hisat2.Alignment.rdg.1,
"', Hisat2.Alignment.rdg.2 = '", Hisat2.Alignment.rdg.2,
"', Hisat2.Alignment.rfg.1 = '", Hisat2.Alignment.rfg.1,
"', Hisat2.Alignment.rfg.2 = '", Hisat2.Alignment.rfg.2,
"', Hisat2.Alignment.score.min.1.function.type = '", Hisat2.Alignment.score.min.1.function.type,
"', Hisat2.Alignment.score.min.2.constant.term = '", Hisat2.Alignment.score.min.2.constant.term,
"', Hisat2.Alignment.score.min.3.coefficient = '", Hisat2.Alignment.score.min.3.coefficient,
"', Hisat2.Alignment.pen.cansplice = '", Hisat2.Alignment.pen.cansplice,
"', Hisat2.Alignment.penc.noncansplice = '", Hisat2.Alignment.penc.noncansplice,
"', Hisat2.Alignment.pen.canintronlen.1.function.type = '", Hisat2.Alignment.pen.canintronlen.1.function.type,
"', Hisat2.Alignment.pen.canintronlen.2.constant.term = '", Hisat2.Alignment.pen.canintronlen.2.constant.term,
"', Hisat2.Alignment.pen.canintronlen.3.coefficient = '", Hisat2.Alignment.pen.canintronlen.3.coefficient,
"', Hisat2.Alignment.pen.noncanintronlen.1.function.type = '", Hisat2.Alignment.pen.noncanintronlen.1.function.type,
"', Hisat2.Alignment.pen.noncanintronlen.2.constant.term = '", Hisat2.Alignment.pen.noncanintronlen.2.constant.term,
"', Hisat2.Alignment.pen.noncanintronlen.3.coefficient = '", Hisat2.Alignment.pen.noncanintronlen.3.coefficient,
"', Hisat2.Alignment.min.intronlen = '", Hisat2.Alignment.min.intronlen,
"', Hisat2.Alignment.max.intronlen = '", Hisat2.Alignment.max.intronlen,
"', Hisat2.Alignment.rna.strandness = '", Hisat2.Alignment.rna.strandness,
"', Hisat2.Alignment.k = '", Hisat2.Alignment.k,
"', Hisat2.Alignment.max.seeds = '", Hisat2.Alignment.max.seeds,
"', Hisat2.Alignment.secondary = ", Hisat2.Alignment.secondary,
", Hisat2.Alignment.minins = '", Hisat2.Alignment.minins,
"', Hisat2.Alignment.maxins = '", Hisat2.Alignment.maxins,
"', Hisat2.Alignment.seed = '", Hisat2.Alignment.seed,
"', STAR.Index.num.parallel.threads = '", STAR.Index.num.parallel.threads,
"', STAR.Index.sjdbOverhang.Read.length = '", STAR.Index.sjdbOverhang.Read.length,
"', STAR.Index.genomeSAindexNbases = '", STAR.Index.genomeSAindexNbases,
"', STAR.Index.genomeChrBinNbits = '", STAR.Index.genomeChrBinNbits,
"', STAR.Index.genomeSAsparseD = '", STAR.Index.genomeSAsparseD,
"', STAR.Alignment.run = ", STAR.Alignment.run,
", STAR.Alignment.num.parallel.threads = '", STAR.Alignment.num.parallel.threads,
"', STAR.Alignment.genomeLoad = '", STAR.Alignment.genomeLoad,
"', STAR.Alignment.readMapNumber = '", STAR.Alignment.readMapNumber,
"', STAR.Alignment.clip3pNbases = '", STAR.Alignment.clip3pNbases,
"', STAR.Alignment.clip5pNbases = '", STAR.Alignment.clip5pNbases,
"', STAR.Alignment.clip3pAdapterSeq = '", STAR.Alignment.clip3pAdapterSeq,
"', STAR.Alignment.clip3pAdapterMMp = '", STAR.Alignment.clip3pAdapterMMp,
"', STAR.Alignment.clip3pAfterAdapterNbases = '", STAR.Alignment.clip3pAfterAdapterNbases,
"', STAR.Alignment.limitGenomeGenerateRAM = '", STAR.Alignment.limitGenomeGenerateRAM,
"', STAR.Alignment.limitIObufferSize = '", STAR.Alignment.limitIObufferSize,
"', STAR.Alignment.limitOutSAMoneReadBytes = '", STAR.Alignment.limitOutSAMoneReadBytes,
"', STAR.Alignment.limitOutSJoneRead = '", STAR.Alignment.limitOutSJoneRead,
"', STAR.Alignment.limitOutSJcollapsed = '", STAR.Alignment.limitOutSJcollapsed,
"', STAR.Alignment.limitBAMsortRAM = '", STAR.Alignment.limitBAMsortRAM,
"', STAR.Alignment.outReadsUnmapped = '", STAR.Alignment.outReadsUnmapped,
"', STAR.Alignment.outQSconversionAdd = '", STAR.Alignment.outQSconversionAdd,
"', STAR.Alignment.outSAMprimaryFlag = '", STAR.Alignment.outSAMprimaryFlag,
"', STAR.Alignment.outSAMmapqUnique = '", STAR.Alignment.outSAMmapqUnique,
"', STAR.Alignment.scoreGap = '", STAR.Alignment.scoreGap,
"', STAR.Alignment.scoreGapNoncan = '", STAR.Alignment.scoreGapNoncan,
"', STAR.Alignment.scoreGapGCAG = '", STAR.Alignment.scoreGapGCAG,
"', STAR.Alignment.scoreGapATAC = '", STAR.Alignment.scoreGapATAC,
"', STAR.Alignment.scoreGenomicLengthLog2scale = '", STAR.Alignment.scoreGenomicLengthLog2scale,
"', STAR.Alignment.scoreDelOpen = '", STAR.Alignment.scoreDelOpen,
"', STAR.Alignment.scoreDelBase = '", STAR.Alignment.scoreDelBase,
"', STAR.Alignment.scoreInsOpen = '", STAR.Alignment.scoreInsOpen,
"', STAR.Alignment.scoreInsBase = '", STAR.Alignment.scoreInsBase,
"', STAR.Alignment.scoreStitchSJshift = '", STAR.Alignment.scoreStitchSJshift,
"', STAR.Alignment.seedSearchStartLmax = '", STAR.Alignment.seedSearchStartLmax,
"', STAR.Alignment.seedSearchStartLmaxOverLread = '", STAR.Alignment.seedSearchStartLmaxOverLread,
"', STAR.Alignment.seedSearchLmax = '", STAR.Alignment.seedSearchLmax,
"', STAR.Alignment.seedMultimapNmax = '", STAR.Alignment.seedMultimapNmax,
"', STAR.Alignment.seedPerReadNmax = '", STAR.Alignment.seedPerReadNmax,
"', STAR.Alignment.seedPerWindowNmax = '", STAR.Alignment.seedPerWindowNmax,
"', STAR.Alignment.seedNoneLociPerWindow = '", STAR.Alignment.seedNoneLociPerWindow,
"', STAR.Alignment.alignIntronMin = '", STAR.Alignment.alignIntronMin,
"', STAR.Alignment.alignIntronMax = '", STAR.Alignment.alignIntronMax,
"', STAR.Alignment.alignMatesGapMax = '", STAR.Alignment.alignMatesGapMax,
"', STAR.Alignment.alignSJoverhangMin = '", STAR.Alignment.alignSJoverhangMin,
"', STAR.Alignment.alignSJDBoverhangMin = '", STAR.Alignment.alignSJDBoverhangMin,
"', STAR.Alignment.alignSplicedMateMapLmin = '", STAR.Alignment.alignSplicedMateMapLmin,
"', STAR.Alignment.alignSplicedMateMapLminOverLmate = '", STAR.Alignment.alignSplicedMateMapLminOverLmate,
"', STAR.Alignment.alignWindowsPerReadNmax = '", STAR.Alignment.alignWindowsPerReadNmax,
"', STAR.Alignment.alignTranscriptsPerWindowNmax = '", STAR.Alignment.alignTranscriptsPerWindowNmax,
"', STAR.Alignment.alignTranscriptsPerReadNmax = '", STAR.Alignment.alignTranscriptsPerReadNmax,
"', STAR.Alignment.alignEndsType = '", STAR.Alignment.alignEndsType,
"', STAR.Alignment.winAnchorMultimapNmax = '", STAR.Alignment.winAnchorMultimapNmax,
"', STAR.Alignment.winBinNbits = '", STAR.Alignment.winBinNbits,
"', STAR.Alignment.winAnchorDistNbins = '", STAR.Alignment.winAnchorDistNbins,
"', STAR.Alignment.winFlankNbins = '", STAR.Alignment.winFlankNbins,
"', Rsamtools.Bam.run = ", Rsamtools.Bam.run,
", Samtools.Bam.num.parallel.threads = '", Samtools.Bam.num.parallel.threads,
"', Rsamtools.nCores = '", Rsamtools.nCores,
"', StringTie.Assemble.run = ", StringTie.Assemble.run,
", Stringtie.Assembly.num.parallel.threads = '", Stringtie.Assembly.num.parallel.threads,
"', Stringtie.Assembly.f = '", Stringtie.Assembly.f,
"', Stringtie.Assembly.m = '", Stringtie.Assembly.m,
"', Stringtie.Assembly.c = '", Stringtie.Assembly.c,
"', Stringtie.Assembly.g = '", Stringtie.Assembly.g,
"', Stringtie.Assembly.M = '", Stringtie.Assembly.M,
"', StringTie.Merge.Trans.run = ", StringTie.Merge.Trans.run,
", Stringtie.Merge.num.parallel.threads = '", Stringtie.Merge.num.parallel.threads,
"', Gffcompare.Ref.Sample.run = ", Gffcompare.Ref.Sample.run,
", StringTie.Ballgown.run = ", StringTie.Ballgown.run,
", Stringtie.2.Ballgown.num.parallel.threads = '", Stringtie.2.Ballgown.num.parallel.threads,
"', PreDECountTable.run = ", PreDECountTable.run,
", check.s4.print = ", check.s4.print, ")")
writeLines(c(first, second), fileConn)
close(fileConn)
message("\u2605 '", path.prefix,
"Rscript/Read_Process.R' has been created.\n")
if (run) {
R.home.lib <- R.home()
R.home.bin <- gsub("/lib/R", "/bin/R", R.home.lib)
system2(command = "nohup",
args = paste0(R.home.bin, " CMD BATCH ",
path.prefix,
"Rscript/Read_Process.R ", path.prefix,
"Rscript_out/Read_Process.Rout"),
stdout = "",
wait = FALSE)
message("\u2605 RNASeq alignment, assembly, quantification, ",
"mergence, comparison, reads process are doing in the ",
"background. Check current progress in '", path.prefix,
"Rscript_out/Read_Process.Rout'\n\n")
}
}
#' @title RNASeqReadProcess
#'
#' @description
#' Process raw reads for RNA-Seq workflow in R shell \cr
#' This function do 5 things : \cr
#' \enumerate{
#' \item 'Hisat2' : aligns raw reads to reference genome.
#' If \code{indices.optional} in \code{RNASeqRParam} is
#' \code{FALSE}, Hisat2 indices will be created.\cr
#' \item 'Rsamtools': converts '.sam' files to '.bam' files.\cr
#' \item 'Stringtie': assembles alignments into transcript.\cr
#' \item 'Gffcompare': examines how transcripts compare with the
#' reference annotation. \cr
#' \item 'Stringtie': creates input files for ballgown, edgeR and DESeq2.\cr
#' \item raw reads count: create raw reads count for DESeq2 and edgeR \cr
#' }
#' Before running this function, \code{RNASeqEnvironmentSet_CMD()} or
#' \code{RNASeqEnvironmentSet()} must be executed successfully.
#' If you want to process raw reads for the following RNA-Seq workflow in
#' background, please see \code{RNASeqReadProcess_CMD()} function.
#'
#' @param RNASeqRParam S4 object instance of experiment-related
#' parameters
#' @param which.trigger Default value is \code{OUTSIDE}. User should not change
#' this value.
#' @param INSIDE.path.prefix Default value is \code{NA}. User should not change
#' this value.
#' @param SAMtools.or.Rsamtools Default value is \code{Rsamtools}. User can set
#' to \code{SAMtools} to use command-line-based 'samtools' instead.
#' @param Hisat2.Index.run Whether to run 'HISAT2 index' step in this function
#' step. Default value is \code{TRUE}. Set \code{FALSE} to skip
#' 'HISAT2 index' step.
#' @param Hisat2.Index.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Hisat2 index step. The default is \code{"1"}
#' @param Hisat2.Index.large.index Hisat2 index terminal '--large-index' option.
#' Default value is \code{FALSE}
#' @param Hisat2.Index.local.ftab.chars Hisat2 index terminal '-t/--ftabchars'
#' option. Default value is \code{"6"}
#' @param Hisat2.Index.local.off.rate Hisat2 index terminal '--localoffrate'
#' option. Default value is \code{"3"}
#' @param Hisat2.Index.ftab.chars Hisat2 index terminal '--localftabchars'
#' option. Default value is \code{"10"}
#' @param Hisat2.Index.off.rate Hisat2 index terminal '--offrate' option.
#' Default value is \code{"4"}
#' @param Hisat2.Alignment.run Whether to run 'HISAT2 alignment' step in this
#' function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'HISAT2 alignment' step.
#' @param Hisat2.Alignment.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Hisat2 alignment step. The default is \code{"1"}
#' @param Hisat2.Alignment.skip Hisat2 alignment terminal '-s/--skip' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.trim5 Hisat2 alignment terminal '-5/--trim5' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.trim3 Hisat2 alignment terminal '-3/--trim3' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.n.ceil.1.function.type Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"L"}
#' @param Hisat2.Alignment.n.ceil.2.constant.term Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"0"}
#' @param Hisat2.Alignment.n.ceil.3.coefficient Hisat2 alignment terminal
#' '--n-ceil' option. Default value is \code{"0.15"}
#' @param Hisat2.Alignment.mp.MX Hisat2 alignment terminal '--mp MX' option.
#' Default value is \code{"6"}
#' @param Hisat2.Alignment.mp.MN Hisat2 alignment terminal '--mp MN' option.
#' Default value is \code{"2"}
#' @param Hisat2.Alignment.sp.MX Hisat2 alignment terminal '--sp MX' option.
#' Default value is \code{"2"}
#' @param Hisat2.Alignment.sp.MN Hisat2 alignment terminal '--sp MN' option.
#' Default value is \code{"1"}
#' @param Hisat2.Alignment.np Hisat2 alignment terminal '--np' option.
#' Default value is \code{"1"}
#' @param Hisat2.Alignment.rdg.1 Hisat2 alignment terminal '--rdg' first option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.rdg.2 Hisat2 alignment terminal '--rdg' first option.
#' Default value is \code{"3"}
#' @param Hisat2.Alignment.rfg.1 Hisat2 alignment terminal '--rfg' first option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.rfg.2 Hisat2 alignment terminal '--rfg' first option.
#' Default value is \code{"3"}
#' @param Hisat2.Alignment.score.min.1.function.type Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"L"}
#' @param Hisat2.Alignment.score.min.2.constant.term Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"0"}
#' @param Hisat2.Alignment.score.min.3.coefficient Hisat2 alignment terminal
#' '--rdg' first option. Default value is \code{"-0.2"}
#' @param Hisat2.Alignment.pen.cansplice Hisat2 alignment terminal
#' '--pen-cansplice' first option. Default value is \code{"-0"}
#' @param Hisat2.Alignment.penc.noncansplice Hisat2 alignment terminal
#' '--pen-noncansplice' option. Default value is \code{"12"}
#' @param Hisat2.Alignment.pen.canintronlen.1.function.type Hisat2 alignment
#' terminal '--pen-canintronlen' first option. Default value is \code{"G"}
#' @param Hisat2.Alignment.pen.canintronlen.2.constant.term Hisat2 alignment
#' terminal '--pen-canintronlen' second option. Default value is \code{"-8"}
#' @param Hisat2.Alignment.pen.canintronlen.3.coefficient Hisat2 alignment
#' terminal '--pen-canintronlen' third option. Default value is \code{"1"}
#' @param Hisat2.Alignment.pen.noncanintronlen.1.function.type Hisat2 alignment
#' terminal '--pen-noncanintronlen' first option. Default value is \code{"G"}
#' @param Hisat2.Alignment.pen.noncanintronlen.2.constant.term Hisat2 alignment
#' terminal '--pen-noncanintronlen' second option. Default value is \code{"-8"}
#' @param Hisat2.Alignment.pen.noncanintronlen.3.coefficient Hisat2 alignment
#' terminal '--pen-noncanintronlen' third option. Default value is \code{"1"}
#' @param Hisat2.Alignment.min.intronlen Hisat2 alignment terminal
#' '--min-intronlen' option. Default value is \code{"20"}
#' @param Hisat2.Alignment.max.intronlen Hisat2 alignment terminal '--max-intronlen'
#' option. Default value is \code{"20"}
#' @param Hisat2.Alignment.rna.strandness Hisat2 alignment terminal '--rna-strandness'
#' option. Default value is \code{"None"}
#' @param Hisat2.Alignment.k Hisat2 alignment terminal '-k' option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.max.seeds Hisat2 alignment terminal '--max-seeds' option.
#' Default value is \code{"5"}
#' @param Hisat2.Alignment.secondary Hisat2 alignment terminal '--secondary' option.
#' Default value is \code{"FALSE"}
#' @param Hisat2.Alignment.minins Hisat2 alignment terminal '-I/--minins' option.
#' Default value is \code{"0"}
#' @param Hisat2.Alignment.maxins Hisat2 alignment terminal '-X/--maxins' option.
#' Default value is \code{"500"}
#' @param Hisat2.Alignment.seed Hisat2 alignment terminal '-X/--maxins' option.
#' Default value is \code{"0"}
#' @param STAR.Index.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for STAR index step. The default is \code{"1"}
#' @param STAR.Index.sjdbOverhang.Read.length STAR index terminal
#' '--sjdbOverhang' option. Default value is \code{"100"}
#' @param STAR.Index.genomeSAindexNbases STAR index terminal
#' '--genomeSAindexNbases' option. Default value is \code{"14"}
#' @param STAR.Index.genomeChrBinNbits STAR index terminal
#' '--genomeChrBinNbits' option. Default value is \code{"18"}
#' @param STAR.Index.genomeSAsparseD STAR index terminal
#' '--genomeSAsparseD' option. Default value is \code{"1"}
#' @param STAR.Alignment.run Whether to run 'STAR index' step in this function
#' step. Default value is \code{FALSE}. Set \code{TRUE} to run STAR alignment step.
#' (need to set Hisat2.Index.run to \code{FALSE})
#' @param STAR.Alignment.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for STAR alignment step. The default is \code{"1"}
#' @param STAR.Alignment.genomeLoad STAR alignment terminal '--genomeLoad'
#' option. Default value is \code{"NoSharedMemory"}
#' @param STAR.Alignment.readMapNumber STAR alignment terminal '--readMapNumber'
#' option. Default value is \code{"-1"}
#' @param STAR.Alignment.clip3pNbases STAR alignment terminal '--clip3pNbases'
#' option. Default value is \code{"0"}
#' @param STAR.Alignment.clip5pNbases STAR alignment terminal '--clip5pNbases'
#' option. Default value is \code{"0"}
#' @param STAR.Alignment.clip3pAdapterSeq STAR alignment terminal '--clip3pAdapterSeq'
#' option. Default value is \code{"-"}
#' @param STAR.Alignment.clip3pAdapterMMp STAR alignment terminal '--clip3pAdapterMMp'
#' option. Default value is \code{"0.1"}
#' @param STAR.Alignment.clip3pAfterAdapterNbases STAR alignment terminal
#' '--clip3pAfterAdapterNbases' option. Default value is \code{"0"}
#' @param STAR.Alignment.limitGenomeGenerateRAM STAR alignment terminal
#' '--limitGenomeGenerateRAM' option. Default value is \code{"31000000000"}
#' @param STAR.Alignment.limitIObufferSize STAR alignment terminal
#' '--limitIObufferSize' option. Default value is \code{"150000000"}
#' @param STAR.Alignment.limitOutSAMoneReadBytes STAR alignment terminal
#' '--limitOutSAMoneReadBytes' option. Default value is \code{"100000"}
#' @param STAR.Alignment.limitOutSJoneRead STAR alignment terminal
#' '--limitOutSJoneRead' option. Default value is \code{"1000"}
#' @param STAR.Alignment.limitOutSJcollapsed STAR alignment terminal
#' '--limitOutSJcollapsed' option. Default value is \code{"1000000"}
#' @param STAR.Alignment.limitBAMsortRAM STAR alignment terminal
#' '--limitBAMsortRAM' option. Default value is \code{"0"}
#' @param STAR.Alignment.outReadsUnmapped STAR alignment terminal
#' '--outReadsUnmapped' option. Default value is \code{"None"}
#' @param STAR.Alignment.outQSconversionAdd STAR alignment terminal
#' '--outQSconversionAdd' option. Default value is \code{"0"}
#' @param STAR.Alignment.outSAMprimaryFlag STAR alignment terminal
#' '--outSAMprimaryFlag' option. Default value is \code{"OneBestScore"}
#' @param STAR.Alignment.outSAMmapqUnique STAR alignment terminal
#' '--outSAMmapqUnique' option. Default value is \code{"255"}
#' @param STAR.Alignment.scoreGap STAR alignment terminal
#' '--scoreGap' option. Default value is \code{"0"}
#' @param STAR.Alignment.scoreGapNoncan STAR alignment terminal
#' '--scoreGapNoncan' option. Default value is \code{"-8"}
#' @param STAR.Alignment.scoreGapGCAG STAR alignment terminal
#' '--scoreGapGCAG' option. Default value is \code{"-4"}
#' @param STAR.Alignment.scoreGapATAC STAR alignment terminal
#' '--scoreGapATAC' option. Default value is \code{"-8"}
#' @param STAR.Alignment.scoreGenomicLengthLog2scale STAR alignment terminal
#' '--scoreGenomicLengthLog2scale' option. Default value is \code{"-0.25"}
#' @param STAR.Alignment.scoreDelOpen STAR alignment terminal
#' '--scoreDelOpen' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreDelBase STAR alignment terminal
#' '--scoreDelBase' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreInsOpen STAR alignment terminal
#' '--scoreInsOpen' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreInsBase STAR alignment terminal
#' '--scoreInsBase' option. Default value is \code{"-2"}
#' @param STAR.Alignment.scoreStitchSJshift STAR alignment terminal
#' '--scoreStitchSJshift' option. Default value is \code{"1"}
#' @param STAR.Alignment.seedSearchStartLmax STAR alignment terminal
#' '--scoreStitchSJshift' option. Default value is \code{"50"}
#' @param STAR.Alignment.seedSearchStartLmaxOverLread STAR alignment terminal
#' '--seedSearchStartLmaxOverLread' option. Default value is \code{"1.0"}
#' @param STAR.Alignment.seedSearchLmax STAR alignment terminal
#' '--seedSearchLmax' option. Default value is \code{"0"}
#' @param STAR.Alignment.seedMultimapNmax STAR alignment terminal
#' '--seedMultimapNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.seedPerReadNmax STAR alignment terminal
#' '--seedPerReadNmax' option. Default value is \code{"1000"}
#' @param STAR.Alignment.seedPerWindowNmax STAR alignment terminal
#' '--seedPerWindowNmax' option. Default value is \code{"50"}
#' @param STAR.Alignment.seedNoneLociPerWindow STAR alignment terminal
#' '--seedNoneLociPerWindow' option. Default value is \code{"10"}
#' @param STAR.Alignment.alignIntronMin STAR alignment terminal
#' '--alignIntronMin' option. Default value is \code{"21"}
#' @param STAR.Alignment.alignIntronMax STAR alignment terminal
#' '--alignIntronMax' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignMatesGapMax STAR alignment terminal
#' '--alignMatesGapMax' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignSJoverhangMin STAR alignment terminal
#' '--alignSJoverhangMin' option. Default value is \code{"5"}
#' @param STAR.Alignment.alignSJDBoverhangMin STAR alignment terminal
#' '--alignSJDBoverhangMin' option. Default value is \code{"3"}
#' @param STAR.Alignment.alignSplicedMateMapLmin STAR alignment terminal
#' '--alignSplicedMateMapLmin' option. Default value is \code{"0"}
#' @param STAR.Alignment.alignSplicedMateMapLminOverLmate STAR alignment terminal
#' '--alignSplicedMateMapLminOverLmate' option. Default value is \code{"0.66"}
#' @param STAR.Alignment.alignWindowsPerReadNmax STAR alignment terminal
#' '--alignWindowsPerReadNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.alignTranscriptsPerWindowNmax STAR alignment terminal
#' '--alignTranscriptsPerWindowNmax' option. Default value is \code{"100"}
#' @param STAR.Alignment.alignTranscriptsPerReadNmax STAR alignment terminal
#' '--alignTranscriptsPerReadNmax' option. Default value is \code{"10000"}
#' @param STAR.Alignment.alignEndsType STAR alignment terminal
#' '--alignEndsType' option. Default value is \code{"Local"}
#' @param STAR.Alignment.winAnchorMultimapNmax STAR alignment terminal
#' '--winAnchorMultimapNmax' option. Default value is \code{"50"}
#' @param STAR.Alignment.winBinNbits STAR alignment terminal
#' '--winBinNbits' option. Default value is \code{"16"}
#' @param STAR.Alignment.winAnchorDistNbins STAR alignment terminal
#' '--winAnchorDistNbins' option. Default value is \code{"9"}
#' @param STAR.Alignment.winFlankNbins STAR alignment terminal
#' '--winFlankNbins' option. Default value is \code{"4"}
#' @param Rsamtools.Bam.run Whether to run 'Rsamtools SAM to BAM' step in this
#' function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'Rsamtools SAM to BAM' step.
#' @param Samtools.Bam.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Samtools sam to bam step. The default is \code{"1"}
#' @param Rsamtools.nCores The number of cores to use when running
#' 'Rsamtools' step. Default value is \code{1}
#' @param StringTie.Assemble.run Whether to run 'StringTie assembly' step in
#' this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie assembly' step.
#' @param Stringtie.Assembly.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie assembly. The default is \code{"1"}
#' @param Stringtie.Assembly.f Stringtie assembly terminal
#' '-f' option. Default value is \code{"0.1"}
#' @param Stringtie.Assembly.m Stringtie assembly terminal
#' '-m' option. Default value is \code{"200"}
#' @param Stringtie.Assembly.c Stringtie assembly terminal
#' '-c' option. Default value is \code{"2.5"}
#' @param Stringtie.Assembly.g Stringtie assembly terminal
#' '-g' option. Default value is \code{"50"}
#' @param Stringtie.Assembly.M Stringtie assembly terminal
#' '-M' option. Default value is \code{"0.95"}
#' @param StringTie.Merge.Trans.run Whether to run 'StringTie GTF merging' step
#' in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie GTF merging' step.
#' @param Stringtie.Merge.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie merge step. The default is \code{"1"}
#' @param Gffcompare.Ref.Sample.run Whether to run 'Gffcompare comparison' step
#' in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'Gffcompare comparison' step.
#' @param StringTie.Ballgown.run Whether to run 'StringTie ballgown creation'
#' step in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'StringTie ballgown creation' step.
#' @param Stringtie.2.Ballgown.num.parallel.threads Specify the number of processing
#' threads (CPUs) to use for Stringtie to ballgown step. The default is \code{"1"}
#' @param PreDECountTable.run Whether to run 'gene raw reads count creation'
#' step in this function step. Default value is \code{TRUE}.
#' Set \code{FALSE} to skip 'gene raw reads count creation' step.
#' @param check.s4.print Default \code{TRUE}. If \code{TRUE},
#' the result of checking \code{RNASeqRParam}
#' will be reported in 'Rscript_out/Environment_Set.Rout'. If \code{FALSE},
#' the result of checking \code{RNASeqRParam} will not be in
#' 'Rscript_out/Environment_Set.Rout'.
#'
#' @return None
#' @export
#' @author Kuan-Hao Chao
#' @examples
#' data(yeast)
#' \dontrun{
#' ## Before run this function, make sure \code{RNASeqEnvironmentSet_CMD()}
#' ##(or\code{RNASeqEnvironmentSet()}) is executed successfully.
#' RNASeqReadProcess(RNASeqRParam = yeast,
#' num.parallel.threads = 10)}
# Parameters: 120
RNASeqReadProcess <- function(RNASeqRParam,
which.trigger = "OUTSIDE",
INSIDE.path.prefix = NA,
SAMtools.or.Rsamtools = "Rsamtools",
Hisat2.Index.run = TRUE,
Hisat2.Index.num.parallel.threads = "1",
Hisat2.Index.large.index = FALSE,
Hisat2.Index.local.ftab.chars = "6",
Hisat2.Index.local.off.rate = "3",
Hisat2.Index.ftab.chars = "10",
Hisat2.Index.off.rate = "4",
Hisat2.Alignment.run = TRUE,
Hisat2.Alignment.num.parallel.threads = "1",
Hisat2.Alignment.skip = "0",
Hisat2.Alignment.trim5 = "0",
Hisat2.Alignment.trim3 = "0",
Hisat2.Alignment.n.ceil.1.function.type = "L",
Hisat2.Alignment.n.ceil.2.constant.term = "0",
Hisat2.Alignment.n.ceil.3.coefficient = "0.15",
Hisat2.Alignment.mp.MX = "6",
Hisat2.Alignment.mp.MN = "2",
Hisat2.Alignment.sp.MX = "2",
Hisat2.Alignment.sp.MN = "1",
Hisat2.Alignment.np = "1",
Hisat2.Alignment.rdg.1 = "5",
Hisat2.Alignment.rdg.2 = "3",
Hisat2.Alignment.rfg.1 = "5",
Hisat2.Alignment.rfg.2 = "3",
Hisat2.Alignment.score.min.1.function.type = "L",
Hisat2.Alignment.score.min.2.constant.term = "0",
Hisat2.Alignment.score.min.3.coefficient = "-0.2",
Hisat2.Alignment.pen.cansplice = "0",
Hisat2.Alignment.penc.noncansplice = "12",
Hisat2.Alignment.pen.canintronlen.1.function.type = "G",
Hisat2.Alignment.pen.canintronlen.2.constant.term = "-8",
Hisat2.Alignment.pen.canintronlen.3.coefficient = "1",
Hisat2.Alignment.pen.noncanintronlen.1.function.type = "G",
Hisat2.Alignment.pen.noncanintronlen.2.constant.term = "-8",
Hisat2.Alignment.pen.noncanintronlen.3.coefficient = "1",
Hisat2.Alignment.min.intronlen = "20",
Hisat2.Alignment.max.intronlen = "500000",
Hisat2.Alignment.rna.strandness = "None",
Hisat2.Alignment.k = "5",
Hisat2.Alignment.max.seeds = "5",
Hisat2.Alignment.secondary = FALSE,
Hisat2.Alignment.minins = "0",
Hisat2.Alignment.maxins = "500",
Hisat2.Alignment.seed = "0",
STAR.Index.num.parallel.threads = "1",
STAR.Index.sjdbOverhang.Read.length = "100",
STAR.Index.genomeSAindexNbases = "14",
STAR.Index.genomeChrBinNbits = "18",
STAR.Index.genomeSAsparseD = "1",
STAR.Alignment.run = FALSE,
STAR.Alignment.num.parallel.threads = "1",
STAR.Alignment.genomeLoad = "NoSharedMemory",
STAR.Alignment.readMapNumber = "-1",
STAR.Alignment.clip3pNbases = "0",
STAR.Alignment.clip5pNbases = "0",
STAR.Alignment.clip3pAdapterSeq = "-",
STAR.Alignment.clip3pAdapterMMp = "0.1",
STAR.Alignment.clip3pAfterAdapterNbases = "0",
STAR.Alignment.limitGenomeGenerateRAM = "31000000000",
STAR.Alignment.limitIObufferSize = "150000000",
STAR.Alignment.limitOutSAMoneReadBytes = "100000",
STAR.Alignment.limitOutSJoneRead = "1000",
STAR.Alignment.limitOutSJcollapsed = "1000000",
STAR.Alignment.limitBAMsortRAM = "0",
STAR.Alignment.outReadsUnmapped = "None",
STAR.Alignment.outQSconversionAdd = "0",
STAR.Alignment.outSAMprimaryFlag = "OneBestScore",
STAR.Alignment.outSAMmapqUnique = "255",
STAR.Alignment.scoreGap = "0",
STAR.Alignment.scoreGapNoncan = "-8",
STAR.Alignment.scoreGapGCAG = "-4",
STAR.Alignment.scoreGapATAC = "-8",
STAR.Alignment.scoreGenomicLengthLog2scale = "-0.25",
STAR.Alignment.scoreDelOpen = "-2",
STAR.Alignment.scoreDelBase = "-2",
STAR.Alignment.scoreInsOpen = "-2",
STAR.Alignment.scoreInsBase = "-2",
STAR.Alignment.scoreStitchSJshift = "1",
STAR.Alignment.seedSearchStartLmax = "50",
STAR.Alignment.seedSearchStartLmaxOverLread = "1.0",
STAR.Alignment.seedSearchLmax = "0",
STAR.Alignment.seedMultimapNmax = "10000",
STAR.Alignment.seedPerReadNmax = "1000",
STAR.Alignment.seedPerWindowNmax = "50",
STAR.Alignment.seedNoneLociPerWindow = "10",
STAR.Alignment.alignIntronMin = "21",
STAR.Alignment.alignIntronMax = "0",
STAR.Alignment.alignMatesGapMax = "0",
STAR.Alignment.alignSJoverhangMin = "5",
STAR.Alignment.alignSJDBoverhangMin = "3",
STAR.Alignment.alignSplicedMateMapLmin = "0",
STAR.Alignment.alignSplicedMateMapLminOverLmate = "0.66",
STAR.Alignment.alignWindowsPerReadNmax = "10000",
STAR.Alignment.alignTranscriptsPerWindowNmax = "100",
STAR.Alignment.alignTranscriptsPerReadNmax = "10000",
STAR.Alignment.alignEndsType = "Local",
STAR.Alignment.winAnchorMultimapNmax = "50",
STAR.Alignment.winBinNbits = "16",
STAR.Alignment.winAnchorDistNbins = "9",
STAR.Alignment.winFlankNbins = "4",
Rsamtools.Bam.run = TRUE,
Samtools.Bam.num.parallel.threads = "1",
Rsamtools.nCores = "1",
StringTie.Assemble.run = TRUE,
Stringtie.Assembly.num.parallel.threads = "1",
Stringtie.Assembly.f = "0.1",
Stringtie.Assembly.m = "200",
Stringtie.Assembly.c = "2.5",
Stringtie.Assembly.g = "50",
Stringtie.Assembly.M = "0.95",
StringTie.Merge.Trans.run = TRUE,
Stringtie.Merge.num.parallel.threads = "1",
Gffcompare.Ref.Sample.run = TRUE,
StringTie.Ballgown.run = TRUE,
Stringtie.2.Ballgown.num.parallel.threads = "1",
PreDECountTable.run = TRUE,
check.s4.print = TRUE) {
CheckOperatingSystem(FALSE)
if (SAMtools.or.Rsamtools != "Rsamtools" &
SAMtools.or.Rsamtools != "SAMtools") {
stop("'SAMtools.or.Rsamtools' must be 'Rsamtools' or 'SAMtools'!!")
}
# If `which.trigger` is OUTSIDE, then directory must be built
# If `which.trigger` is INSIDE, then directory must not be
# built here(will created in CMD)
if (isS4(RNASeqRParam) &
which.trigger == "OUTSIDE" &
is.na(INSIDE.path.prefix)) {
# This is an external call!!
# Check the S4 object(user input)
} else if (RNASeqRParam == "INSIDE" &
which.trigger == "INSIDE" &
!is.na(INSIDE.path.prefix)) {
# This is an internal call!!
# Load the S4 object that saved in CMD process
RNASeqRParam <- readRDS(paste0(INSIDE.path.prefix,
"gene_data/RNASeqRParam.rds"))
}
which.s4.object <- CheckS4Object_All(RNASeqRParam, check.s4.print)
# To find 'HISAT2', 'StringTie' and 'Gffcompare'
path.prefix <- "@"(RNASeqRParam, path.prefix)
input.path.prefix <- "@"(RNASeqRParam, input.path.prefix)
genome.name <- "@"(RNASeqRParam, genome.name)
sample.pattern <- "@"(RNASeqRParam, sample.pattern)
independent.variable <- "@"(RNASeqRParam, independent.variable)
case.group <- "@"(RNASeqRParam, case.group)
control.group <- "@"(RNASeqRParam, control.group)
python.variable <- "@"(RNASeqRParam, python.variable)
python.variable.answer <- python.variable$check.answer
python.variable.version <- python.variable$python.version
python.2to3 <- "@"(RNASeqRParam, python.2to3)
fastq.gz.type <- "@"(RNASeqRParam, fastq.gz.type)
ExportPath(path.prefix)
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
if (which.s4.object == "RNASeqRParam") {
indices.optional <- "@"(RNASeqRParam, indices.optional)
PreRNASeqReadProcess(path.prefix, genome.name, sample.pattern)
# Check alignemnt selection first !
if (isTRUE(Hisat2.Alignment.run) && isTRUE(STAR.Alignment.run)) {
stop("Hisat2 and STAR can not run at the same time !")
} else if (isTRUE(Hisat2.Alignment.run) && !isTRUE(STAR.Alignment.run)) {
message("Hisat2 is selected as aligner in the pipeline !")
} else if (!isTRUE(Hisat2.Alignment.run) && isTRUE(STAR.Alignment.run)) {
message("STAR is selected as aligner in the pipeline !")
}
if (check.results$ht2.files.number.df == 0 &&
!indices.optional & Hisat2.Index.run) {
# Parameters: 11
CreateHisat2Index(path.prefix,
genome.name,
sample.pattern,
splice.site.info = TRUE,
exon.info = TRUE,
Hisat2.Index.num.parallel.threads,
Hisat2.Index.large.index,
Hisat2.Index.local.ftab.chars,
Hisat2.Index.local.off.rate,
Hisat2.Index.ftab.chars,
Hisat2.Index.off.rate)
}
if (Hisat2.Alignment.run) {
# Parameters: 43
Hisat2AlignmentDefault(path.prefix,
fastq.gz.type,
genome.name,
sample.pattern,
independent.variable,
case.group,
control.group,
Hisat2.Alignment.num.parallel.threads,
Hisat2.Alignment.skip,
Hisat2.Alignment.trim5,
Hisat2.Alignment.trim3,
Hisat2.Alignment.n.ceil.1.function.type,
Hisat2.Alignment.n.ceil.2.constant.term,
Hisat2.Alignment.n.ceil.3.coefficient,
Hisat2.Alignment.mp.MX,
Hisat2.Alignment.mp.MN,
Hisat2.Alignment.sp.MX,
Hisat2.Alignment.sp.MN,
Hisat2.Alignment.np,
Hisat2.Alignment.rdg.1,
Hisat2.Alignment.rdg.2,
Hisat2.Alignment.rfg.1,
Hisat2.Alignment.rfg.2,
Hisat2.Alignment.score.min.1.function.type,
Hisat2.Alignment.score.min.2.constant.term,
Hisat2.Alignment.score.min.3.coefficient,
Hisat2.Alignment.pen.cansplice,
Hisat2.Alignment.penc.noncansplice,
Hisat2.Alignment.pen.canintronlen.1.function.type,
Hisat2.Alignment.pen.canintronlen.2.constant.term,
Hisat2.Alignment.pen.canintronlen.3.coefficient,
Hisat2.Alignment.pen.noncanintronlen.1.function.type,
Hisat2.Alignment.pen.noncanintronlen.2.constant.term,
Hisat2.Alignment.pen.noncanintronlen.3.coefficient,
Hisat2.Alignment.min.intronlen,
Hisat2.Alignment.max.intronlen,
Hisat2.Alignment.rna.strandness,
Hisat2.Alignment.k,
Hisat2.Alignment.max.seeds,
Hisat2.Alignment.secondary,
Hisat2.Alignment.minins,
Hisat2.Alignment.maxins,
Hisat2.Alignment.seed)
}
if (STAR.Alignment.run) {
# Parameters: 8
CreateSTARIndex(path.prefix,
genome.name,
sample.pattern,
STAR.Index.num.parallel.threads,
STAR.Index.sjdbOverhang.Read.length,
STAR.Index.genomeSAindexNbases,
STAR.Index.genomeChrBinNbits,
STAR.Index.genomeSAsparseD)
# Parameters: 53
STARAlignmentDefault(path.prefix,
fastq.gz.type,
genome.name,
sample.pattern,
STAR.Alignment.num.parallel.threads,
STAR.Alignment.genomeLoad,
STAR.Alignment.readMapNumber,
STAR.Alignment.clip3pNbases,
STAR.Alignment.clip5pNbases,
STAR.Alignment.clip3pAdapterSeq,
STAR.Alignment.clip3pAdapterMMp,
STAR.Alignment.clip3pAfterAdapterNbases,
STAR.Alignment.limitGenomeGenerateRAM,
STAR.Alignment.limitIObufferSize,
STAR.Alignment.limitOutSAMoneReadBytes,
STAR.Alignment.limitOutSJoneRead,
STAR.Alignment.limitOutSJcollapsed,
STAR.Alignment.limitBAMsortRAM,
STAR.Alignment.outReadsUnmapped,
STAR.Alignment.outQSconversionAdd,
STAR.Alignment.outSAMprimaryFlag,
STAR.Alignment.outSAMmapqUnique,
STAR.Alignment.scoreGap,
STAR.Alignment.scoreGapNoncan,
STAR.Alignment.scoreGapGCAG,
STAR.Alignment.scoreGapATAC,
STAR.Alignment.scoreGenomicLengthLog2scale,
STAR.Alignment.scoreDelOpen,
STAR.Alignment.scoreDelBase,
STAR.Alignment.scoreInsOpen,
STAR.Alignment.scoreInsBase,
STAR.Alignment.scoreStitchSJshift,
STAR.Alignment.seedSearchStartLmax,
STAR.Alignment.seedSearchStartLmaxOverLread,
STAR.Alignment.seedSearchLmax,
STAR.Alignment.seedMultimapNmax,
STAR.Alignment.seedPerReadNmax,
STAR.Alignment.seedPerWindowNmax,
STAR.Alignment.seedNoneLociPerWindow,
STAR.Alignment.alignIntronMin,
STAR.Alignment.alignIntronMax,
STAR.Alignment.alignMatesGapMax,
STAR.Alignment.alignSJoverhangMin,
STAR.Alignment.alignSJDBoverhangMin,
STAR.Alignment.alignSplicedMateMapLmin,
STAR.Alignment.alignSplicedMateMapLminOverLmate,
STAR.Alignment.alignWindowsPerReadNmax,
STAR.Alignment.alignTranscriptsPerWindowNmax,
STAR.Alignment.alignTranscriptsPerReadNmax,
STAR.Alignment.alignEndsType,
STAR.Alignment.winAnchorMultimapNmax,
STAR.Alignment.winBinNbits,
STAR.Alignment.winAnchorDistNbins,
STAR.Alignment.winFlankNbins)
}
if (Rsamtools.Bam.run) {
# Parameters: 6
RSamtoolsToBam(SAMtools.or.Rsamtools,
Samtools.Bam.num.parallel.threads,
path.prefix,
genome.name,
sample.pattern,
Rsamtools.nCores)
}
} else if (which.s4.object == "RNASeqRParam_Sam") {
PreRNASeqReadProcess_Sam(path.prefix, genome.name, sample.pattern)
if (Rsamtools.Bam.run) {
# Parameters: 6
RSamtoolsToBam(SAMtools.or.Rsamtools,
Samtools.Bam.num.parallel.threads,
path.prefix,
genome.name,
sample.pattern,
Rsamtools.nCores)
}
} else if (which.s4.object == "RNASeqRParam_Bam") {
PreRNASeqReadProcess_Bam(path.prefix, genome.name, sample.pattern)
}
if (StringTie.Assemble.run) {
# Parameters: 9
StringTieAssemble(path.prefix,
genome.name,
sample.pattern,
Stringtie.Assembly.num.parallel.threads,
Stringtie.Assembly.f,
Stringtie.Assembly.m,
Stringtie.Assembly.c,
Stringtie.Assembly.g,
Stringtie.Assembly.M)
}
if (StringTie.Merge.Trans.run) {
# Parameters: 4
StringTieMergeTrans(path.prefix,
genome.name,
sample.pattern,
Stringtie.Merge.num.parallel.threads)
}
if (Gffcompare.Ref.Sample.run) {
# Parameters: 3
GffcompareRefSample(path.prefix,
genome.name,
sample.pattern)
}
if (StringTie.Ballgown.run) {
# Parameters: 4
StringTieToBallgown(path.prefix,
genome.name,
sample.pattern,
Stringtie.2.Ballgown.num.parallel.threads)
}
finals <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=TRUE)
if (PreDECountTable.run &
((python.variable.answer & python.variable.version == 2) |
python.variable.answer & python.variable.version == 3 & python.2to3)) {
# Parameters: 6
PreDECountTable(path.prefix,
sample.pattern,
python.variable.answer,
python.variable.version,
python.2to3,
print=TRUE)
}
if (which.s4.object == "RNASeqRParam") {
PostRNASeqReadProcess(path.prefix,
genome.name,
sample.pattern)
} else if (which.s4.object == "RNASeqRParam_Sam") {
PostRNASeqReadProcess_Sam(path.prefix,
genome.name,
sample.pattern)
} else if (which.s4.object == "RNASeqRParam_Bam") {
PostRNASeqReadProcess_Bam(path.prefix,
genome.name,
sample.pattern)
}
}
PreRNASeqReadProcess <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment pre-check ...\n")
phenodata.csv <- file.exists(paste0(path.prefix, "gene_data/phenodata.csv"))
ref.gtf <- file.exists(paste0(path.prefix,
"gene_data/ref_genes/", genome.name, ".gtf"))
ref.fa <- file.exists(paste0(path.prefix,
"gene_data/ref_genome/", genome.name, ".fa"))
raw.fastq <- list.files(path = paste0(path.prefix, 'gene_data/raw_fastq.gz/'),
pattern = sample.pattern,
all.files = FALSE,
full.names = FALSE,
recursive = FALSE,
ignore.case = FALSE)
check.tool.result <- CheckToolAll(path.prefix)
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
check.progress.results.bool <- check.results$gtf.file.logic.df &&
check.results$fa.file.logic.df &&
(check.results$fastq.gz.files.number.df != 0)
validity <- phenodata.csv && ref.gtf && ref.fa && check.tool.result &&
(length(raw.fastq) != 0) && check.progress.results.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() environment ERROR")
}
message("(\u2714) : RNASeqReadProcess() pre-check is valid\n\n")
}
PreRNASeqReadProcess_Sam <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment pre-check ...\n")
phenodata.csv <- file.exists(paste0(path.prefix, "gene_data/phenodata.csv"))
ref.gtf <- file.exists(paste0(path.prefix,
"gene_data/ref_genes/", genome.name, ".gtf"))
raw.sam <- list.files(path = paste0(path.prefix, 'gene_data/raw_sam/'),
pattern = sample.pattern,
all.files = FALSE,
full.names = FALSE,
recursive = FALSE,
ignore.case = FALSE)
check.tool.result <- CheckTool_Sam_Bam(path.prefix)
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
check.progress.results.bool <- check.results$gtf.file.logic.df &&
(check.results$sam.files.number.df != 0)
validity <- phenodata.csv && ref.gtf && check.tool.result &&
(length(raw.sam) != 0) && check.progress.results.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() environment ERROR")
}
message("(\u2714) : RNASeqReadProcess() pre-check is valid\n\n")
}
PreRNASeqReadProcess_Bam <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment pre-check ...\n")
phenodata.csv <- file.exists(paste0(path.prefix, "gene_data/phenodata.csv"))
ref.gtf <- file.exists(paste0(path.prefix,
"gene_data/ref_genes/", genome.name, ".gtf"))
raw.bam <- list.files(path = paste0(path.prefix, 'gene_data/raw_bam/'),
pattern = sample.pattern,
all.files = FALSE,
full.names = FALSE,
recursive = FALSE,
ignore.case = FALSE)
check.tool.result <- CheckTool_Sam_Bam(path.prefix)
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
check.progress.results.bool <- check.results$gtf.file.logic.df &&
(check.results$bam.files.number.df != 0)
validity <- phenodata.csv && ref.gtf && check.tool.result &&
(length(raw.bam) != 0) && check.progress.results.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() environment ERROR")
}
message("(\u2714) : RNASeqReadProcess() pre-check is valid\n\n")
}
PostRNASeqReadProcess <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment post-check ...\n")
# Still need to add condition
gene_abundance <- dir.exists(paste0(path.prefix, "gene_data/gene_abundance/"))
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
ht2.bool <- (check.results$ht2.files.number.df) != 0
sam.bool <- (check.results$sam.files.number.df) != 0
bam.bool <- (check.results$bam.files.number.df) != 0
gtf.bool <- (check.results$gtf.files.number.df) != 0
merged.bool <- check.results$stringtie_merged.gtf.file.df
gffcompare.bool <- (check.results$gffcompare.related.dirs.number.df) != 0
ballgown.bool <- (check.results$ballgown.dirs.number.df) != 0
validity <- gene_abundance && ht2.bool && sam.bool && bam.bool && gtf.bool &&
merged.bool && gffcompare.bool && ballgown.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() post-check ERROR")
}
message("(\u2714) : RNASeqReadProcess() post-check is valid\n\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605 Success!! \u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
}
PostRNASeqReadProcess_Sam <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment post-check ...\n")
# Still need to add condition
gene_abundance <- dir.exists(paste0(path.prefix, "gene_data/gene_abundance/"))
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
sam.bool <- (check.results$sam.files.number.df) != 0
bam.bool <- (check.results$bam.files.number.df) != 0
gtf.bool <- (check.results$gtf.files.number.df) != 0
merged.bool <- check.results$stringtie_merged.gtf.file.df
gffcompare.bool <- (check.results$gffcompare.related.dirs.number.df) != 0
ballgown.bool <- (check.results$ballgown.dirs.number.df) != 0
validity <- gene_abundance && sam.bool && bam.bool && gtf.bool &&
merged.bool && gffcompare.bool && ballgown.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() post-check ERROR")
}
message("(\u2714) : RNASeqReadProcess() post-check is valid\n\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605 Success!! \u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
}
PostRNASeqReadProcess_Bam <- function(path.prefix, genome.name, sample.pattern) {
message("\u269C\u265C\u265C\u265C RNASeqReadProcess()' ",
"environment post-check ...\n")
# Still need to add condition
gene_abundance <- dir.exists(paste0(path.prefix, "gene_data/gene_abundance/"))
check.results <- ProgressGenesFiles(path.prefix,
genome.name,
sample.pattern,
print=FALSE)
bam.bool <- (check.results$bam.files.number.df) != 0
gtf.bool <- (check.results$gtf.files.number.df) != 0
merged.bool <- check.results$stringtie_merged.gtf.file.df
gffcompare.bool <- (check.results$gffcompare.related.dirs.number.df) != 0
ballgown.bool <- (check.results$ballgown.dirs.number.df) != 0
validity <- gene_abundance && bam.bool && gtf.bool &&
merged.bool && gffcompare.bool && ballgown.bool
if (!isTRUE(validity)) {
stop("RNASeqReadProcess() post-check ERROR")
}
message("(\u2714) : RNASeqReadProcess() post-check is valid\n\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605 Success!! \u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\n")
message("\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605",
"\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\u2605\n")
}
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