Nothing
R/easyRNASeq-package.R
In easyRNASeq: Count summarization and normalization for RNA-Seq data
# to re-build the documentation and namespace
# library(roxygen2)
# roxygenize("../easyrnaseq-devel/",roclets=c('rd', 'collate', 'namespace'),clean=TRUE)
# to update the package versions
# pkg <- c("Biobase","BiocGenerics","BiocParallel","biomaRt","Biostrings",
# "DESeq","edgeR","GenomeInfoDb","genomeIntervals",
# "GenomicAlignments","GenomicRanges","SummarizedExperiment",
# "IRanges","LSD","Rsamtools","S4Vectors","ShortRead",
# "BiocStyle","rappdirs,
# "BSgenome",
# "BSgenome.Dmelanogaster.UCSC.dm3","GenomicFeatures",
# "RUnit")
# pkg[! pkg %in% rownames(installed.packages())]
# installed.packages()[pkg,"Version"]
##==========================
## package details
##==========================
#' Count summarization and normalization pipeline for Next Generation Sequencing data.
#'
#' Offers functionalities to summarize read counts per feature of interest, e.g. exons, transcripts, genes, etc.
#' Offers functionalities to normalize the summarized counts using 3rd party packages like \code{\link[DESeq:newCountDataSet]{DESeq}}
#' or \code{\link[edgeR:DGEList]{edgeR}}.
#'
#' @section Methods:
#' The main function \code{\link[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}} will summarize the counts per
#' feature of interest, for as many samples as provided and will return a
#' count matrix (N*M) where N are the features and M the samples.
#' This data can be corrected to \pkg{RPKM} in which case
#' a matrix of corrected value is returned instead, with the same dimensions.
#' Alternatively a \code{\linkS4class{RangedSummarizedExperiment}} can be returned and this
#' is expected to be the default in the upcoming version of easyRNASeq (as of 1.5.x).
#' If the necessary sample
#' information are provided, the data can be normalized using either \code{\link[DESeq:newCountDataSet]{DESeq}}
#' or \code{\link[edgeR:DGEList]{edgeR}} and the corresponding package object returned.
#' For more insider details, and step by step functions, see:
#' \tabular{ll}{
#' \code{\link[easyRNASeq:ShortRead-methods]{ShortRead methods}} for pre-processing the data.
#' \code{\link[easyRNASeq:easyRNASeq-annotation-methods]{easyRNASeq annotation methods}} for getting the annotation.
#' \code{\link[easyRNASeq:easyRNASeq-coverage-methods]{easyRNASeq coverage methods}} for computing the coverage from a Short Read Alignment file.
#' \code{\link[easyRNASeq:easyRNASeq-summarization-methods]{easyRNASeq summarization methods}} for summarizing the data.
#' \code{\link[easyRNASeq:easyRNASeq-correction-methods]{easyRNASeq correction methods}} for correcting the data (i.e. generating RPKM).
#' \code{\link[easyRNASeq:edgeR-methods]{edgeR methods}} for post-processing the data.
#' \code{\link[easyRNASeq:DESeq-methods]{DESeq methods}} for post-processing the data.
#' }
#'
#' @name easyRNASeq package
#' @rdname easyRNASeq-package
#' @aliases easyRNASeq-package assay type BamFileList BamFileList-class IRanges
#' GRanges-class GRanges SRFilterResult SummarizedExperiment RangedSummarizedExperiment-class
#' chromosomeFilter compose nFilter
#' @docType package
#' @author Nicolas Delhomme, Bastian Schiffthaler, Ismael Padioleau
#' @keywords package
#' @seealso
#' The class RNAseq specification:
#' \code{\linkS4class{RNAseq}}
#'
#' The default output class specification:
#' \code{\linkS4class{RangedSummarizedExperiment}}
#'
#' The imported packages:
#' \code{\link[biomaRt:useMart]{biomaRt}}
#' \code{\link[BiocParallel:BiocParallel-package]{BiocParallel}}
#' \code{\link[edgeR:DGEList]{edgeR}}
#' \code{\link[genomeIntervals:Genome_intervals_stranded-class]{genomeIntervals}}
#' \code{\link[Biostrings:XString-class]{Biostrings}}
#' \code{\link[BSgenome:BSgenome-class]{BSgenome}}
#' \code{\link[DESeq:newCountDataSet]{DESeq}}
#' \code{\link[GenomicRanges:GRanges-class]{GenomicRanges}}
#' \code{\link[IRanges:IRanges-constructor]{IRanges}}
#' \code{\link[Rsamtools:scanBam]{Rsamtools}}
#' \code{\link[ShortRead:readAligned]{ShortRead}}
#'
#' The suggested packages:
#' \code{\link[parallel:makeCluster]{parallel}}
#' \code{\link[GenomicFeatures:TxDb-class]{GenomicFeatures}}
#'
#' The following classes and functions that are made available from
#' other packages:
#' \itemize{
#' \item{Classes}{
#' \code{\link[Rsamtools:BamFile-class]{BamFileList-class}}
#' \code{\linkS4class{CountDataSet}}
#' \code{\linkS4class{RangedSummarizedExperiment}}
#' }
#' \item{Functions/Methods}{
#' \code{\link[DESeq:estimateDispersions]{DESeq estimate size factor and
#' estimate dispersion functions}}
#' \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{
#' The RangedSummarizedExperiment assay accessor}
#' }
#' The locfit function \code{\link[locfit]{locfit}}
#' The BamFileList constructor \code{\link[Rsamtools:BamFile-class]{BamFileList-class}}
#' The IRanges constructor \code{\link[IRanges]{IRanges-constructor}}
#' For the SRFilterResult,
#' chromosomeFilter, compose and nFilter methods\code{\link[ShortRead]{srFilter}}
#' }
#' }
#'
#' @examples
#' # the data
#' tdir <- tutorialData()
#'
#' # get the example annotation file - we retrieve a gtf file from GitHub
#' annot <- fetchData("Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz")
#'
#' # create the AnnotParam
#' annotParam <- AnnotParam(
#' datasource=annot,
#' type="gtf")
#'
#' # create the synthetic transcripts
#' annotParam <- createSyntheticTranscripts(annotParam,verbose=FALSE)
#'
#' # create the RnaSeqParam
#' rnaSeqParam <- RnaSeqParam(annotParam=annotParam,countBy="gene")
#'
#' # get the bamfiles (from the Bioc cache in this example)
#' filenames <- dir(tdir,pattern="[A,T].*\\.bam$",full.names=TRUE)
#' indexnames <- sapply(paste0(sub(".*_","",basename(filenames)),".bai"),fetchData)
#' bamFiles <- getBamFileList(filenames,indexnames)
#'
#' # get a RangedSummarizedExperiment containing the counts table
#' sexp <- simpleRNASeq(
#' bamFiles=bamFiles,
#' param=rnaSeqParam,
#' verbose=TRUE
#' )
#'
#' # get the counts
#' assays(sexp)$genes
#'
#'
NULL
##==========================
# To define the NAMESPACE
##==========================
# library(codetoolsBioC)
# library(easyRNASeq)
# writeNamespaceImports("easyRNASeq")
# import classes
#' @importClassesFrom Biostrings DNAStringSet
#' @importClassesFrom DESeq CountDataSet
#' @importClassesFrom edgeR DGEList
#' @importClassesFrom genomeIntervals Genome_intervals Genome_intervals_stranded
#' @importClassesFrom GenomicAlignments GAlignments GAlignmentPairs
#' @importClassesFrom GenomicRanges GRanges GRangesList
#' @importClassesFrom SummarizedExperiment RangedSummarizedExperiment
#' @importClassesFrom IRanges RleList
#' @importClassesFrom S4Vectors Annotated Vector DataFrame SimpleList
#' @importClassesFrom methods ANY character "function" integer
#' list matrix missing numeric vector
#' @importClassesFrom Rsamtools BamFile BamFileList
#' @importClassesFrom ShortRead AlignedRead ShortReadQ
# import S4 methods
#' @importMethodsFrom Biobase fData varMetadata
#' @importFrom BiocFileCache bfcadd bfcdownload bfcneedsupdate bfcquery bfcrpath
#' @importMethodsFrom BiocGenerics annotation cbind clusterApply
#' colnames counts duplicated estimateDispersions estimateSizeFactors
#' eval fileName get intersect lapply match order path paste pmax rbind
#' rownames sapply strand "strand<-" table unique
#' @importMethodsFrom Biostrings type
#' @importMethodsFrom DESeq estimateSizeFactors estimateDispersions
#' @importMethodsFrom genomeIntervals readGff3 writeGff3
#' @importMethodsFrom GenomeInfoDb seqinfo seqlengths "seqlengths<-"
#' seqlevels "seqlevels<-" seqnames "seqnames<-"
#' @importMethodsFrom GenomicAlignments cigar summarizeOverlaps
#' @importMethodsFrom GenomicRanges grglist
#' @importMethodsFrom IRanges as.list as.matrix
#' "colnames<-" countOverlaps coverage end "end<-" findOverlaps
#' gsub mean median narrow nchar ranges reduce "rownames<-" space
#' start "start<-" sub tolower unlist values which width
#' @importMethodsFrom methods coerce initialize show
#' @importMethodsFrom Rsamtools asMates "asMates<-" countBam scanBam
#' scanBamHeader ScanBamParam yieldSize "yieldSize<-"
#' @importMethodsFrom S4Vectors "%in%" as.table elementMetadata
#' "elementMetadata<-" elementNROWS levels mcols metadata
#' "metadata<-" Rle runLength runsum runValue split substr
#' @importMethodsFrom ShortRead chromosome id position readAligned
#' srdistance sread srFilter writeFastq
#' @importMethodsFrom SummarizedExperiment assay assays "assays<-"
#' colData "colData<-" rowRanges "rowRanges<-"
# import methods
#' @importFrom biomaRt getBM listDatasets useDataset useMart
#' @importFrom BiocParallel MulticoreParam SerialParam
#' @importFrom Biostrings DNAStringSet
#' @importFrom DESeq fitInfo newCountDataSet
#' @importFrom edgeR calcNormFactors DGEList estimateCommonDisp
#' estimateTagwiseDisp maPlot plotMDS.DGEList plotMeanVar plotBCV
#' @importFrom genomeIntervals getGffAttribute parseGffAttributes
#' @importFrom GenomicAlignments GAlignments readGAlignments readGAlignmentPairs
#' @importFrom GenomicRanges GRanges GRangesList
#' @importFrom graphics abline axis axTicks boxplot grid hist legend lines
#' mtext par plot rect
#' @importFrom IRanges IRanges IRangesList LogicalList
#' SplitDataFrameList RleList
#' @importFrom locfit locfit lp
#' @importFrom LSD heatscatter
#' @importFrom methods as extends is new
#' @importFrom parallel makePSOCKcluster parLapply stopCluster
#' @importFrom rappdirs user_cache_dir
#' @importFrom Rsamtools BamFileList bamFlagTest index scanBamFlag
#' @importFrom S4Vectors endoapply DataFrame queryHits SimpleList
#' @importFrom ShortRead alignData chromosomeFilter compose nFilter
#' SRFilterResult
#' @importFrom stats aggregate na.omit
#' @importFrom SummarizedExperiment SummarizedExperiment
#' @importFrom utils combn str packageVersion
# and export!
#' @exportClass BamFileList GRanges RangedSummarizedExperiment
#' @exportMethod assay assays colData estimateDispersions estimateSizeFactors fileName metadata rowRanges seqinfo seqlengths seqlevels "seqlevels<-" seqnames "seqnames<-" split srFilter width writeFastq writeGff3
#' @export alignData basename chromosomeFilter compose BamFileList GRanges IRanges locfit lp newCountDataSet nFilter readAligned SRFilterResult SummarizedExperiment
NULL
##==========================
# To detail the deprecation
##==========================
# nothing at the time - copy the defunct block if needed and
# replace defunct by deprecated
##==========================
# To detail defunct function
##==========================
#' The following function are defunct:
#' \itemize{
#' \item \code{\link[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}}
#' \item \code{\link[easyRNASeq:easyRNASeq-coverage-methods]{fetchCoverage}}
#' \item \code{fetchAnnotation}
#' \item \code{knownOrganisms}
#' \item \code{plotDispersionEstimates,DGEList-method}
#' }
#'
#' \itemize{
#' \item The \code{plotDispersionEstimates,DGEList-method}
#' function is superseded by the \code{\link[edgeR:plotBCV]{plotBCV}} function
#' as the \pkg{edgeR} DGEList object structure changed
#' \item The \code{\link[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}} function is superseded by the
#' \code{\link[easyRNASeq:easyRNASeq-simpleRNASeq]{simpleRNASeq}} function to consolidate and
#' prune the overall package. The changes are based on user comments and on the
#' general standardization occuring in the field.
#' \item The \code{\link[easyRNASeq:easyRNASeq-coverage-methods]{fetchCoverage}} function only had two
#' parameters deprecated as the consequence of the package consolidation. As the scanBam
#' function is not called directly anymore but through higher level functions (from the
#' GenomicRanges package), the 'what' and 'isUnmappedQuery' parameters were obsolete.
#' }
#' @aliases plotDispersionEstimates,DGEList-method fetchAnnotation knownOrganisms
#' easyRNASeq easyRNASeq,RNAseq-method fetchCoverage,RNAseq-method fetchCoverage
#' organismName<- organismName organismName,RNAseq-method organismName<-,RNAseq-method
#' @name Defunct functions
#' @rdname easyRNASeq-defunct
NULL
##==========================
# To detail dataset
##==========================
#' Dataset included in the package
#'
#' The package contains a dataset from the \emph{Robinson, Delhomme et al., 2014}
#' publication.
#' \itemize{
#' \item{RobinsonDelhomme2014}{a normalised expression count table. This dataset was
#' generated from 17 \emph{Populus tremula} - Eurasian
#' aspen - trees used to assess the sexual dimorphism of this dioecious species. This
#' count matrix has been generating following published pre-processing
#' guidelines - see \url{http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis} -
#' and the resulting HTSeq files have been collated and the obtained raw count
#' matrix submitted to a variance stabilising transformation. Subsequently, the
#' values have been transformed so that the minimal vst values - that
#' corresponds to an absence of expression - is 0. Hence the counts in the
#' matrix are library-size normalized, variance stabilised expression values,
#' with a minimal value of 0.}
#' }
#' @aliases easyRNASeq-datasets
#' RobinsonDelhomme2014
#' @name easyRNASeq-datasets
#' @rdname easyRNASeq-datasets
#' @keywords data
NULL
##==========================
# To detail hardcoded parameters
##==========================
#' Objects created when the package is attached.
#'
#' The package creates the following objects when attached
#' \itemize{
#' \item GTF.FIELDS
#' \item ANNOTATION.TYPE
#' \item TUTORIAL.DATA
#' \item VIGNETTE.DATA
#' }
#'
#' These objects hold the following information
#' \itemize{
#' \item GTF.FIELDS \code{c("gene_id","transcript_id","exon_id","gene_name")}
#' \item ANNOTATION.TYPE \code{c(mRNA="mRNA",exon="exon")}
#' \item TUTORIAL.DATA: The list of files needed for the help and test
#' pages
#' \item VIGNETTE.DATA: The list of files needed for the vignette
#' }
#' and are designed as global variables to expose the
#' fact that they are hardcoded. These exist as
#' placeholder in case a user would require different
#' values for these.
#'
#' @aliases easyRNASeq-global-variables .onAttach ANNOTATION.TYPE GTF.FIELDS
#' TUTORIAL.DATA VIGNETTE.DATA
#' @name easyRNASeq-global-variables
#' @rdname easyRNASeq-global-variables
#' @param libname a character string giving the library directory where the package defining the namespace was found.
#' @param pkgname a character string giving the name of the package.
#' @seealso \code{\link[base:ns-hooks]{.onAttach}} in the \code{base} package.
#' @keywords internal
globalVariables("GTF.FIELDS")
globalVariables("ANNOTATION.TYPE")
globalVariables("TUTORIAL.DATA")
globalVariables("VIGNETTE.DATA")
".onAttach" <- function(libname,pkgname){
assign("GTF.FIELDS",c("gene_id","transcript_id","exon_id",
"gene_name"),
envir=as.environment("package:easyRNASeq"))
assign("ANNOTATION.TYPE",c(mRNA="mRNA",exon="exon"),
envir=as.environment("package:easyRNASeq"))
.gitHubURL <- "https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq"
assign("TUTORIAL.DATA",
c(ACACTG.bam=file.path(.gitHubURL,"ACACTG.bam"),
ACTAGC.bam=file.path(.gitHubURL,"ACTAGC.bam"),
ATGGCT.bam=file.path(.gitHubURL,"ATGGCT.bam"),
TTGCGA.bam=file.path(.gitHubURL,"TTGCGA.bam"),
ACACTG.bam.bai=file.path(.gitHubURL,"ACACTG.bam.bai"),
ACTAGC.bam.bai=file.path(.gitHubURL,"ACTAGC.bam.bai"),
ATGGCT.bam.bai=file.path(.gitHubURL,"ATGGCT.bam.bai"),
TTGCGA.bam.bai=file.path(.gitHubURL,"TTGCGA.bam.bai"),
"Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz"=
file.path(.gitHubURL,"Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz"),
gAnnot.rda=file.path(.gitHubURL,"gAnnot.rda"),
"Dmel-mRNA-exon-r5.52.gff3.gz"=file.path(.gitHubURL,"Dmel-mRNA-exon-r5.52.gff3.gz")),
envir=as.environment("package:easyRNASeq"))
assign("VIGNETTE.DATA",
c("Ptrichocarpa_210_v3.0_gene_exons.gff3.gz"=
file.path(.gitHubURL,"Ptrichocarpa_210_v3.0_gene_exons.gff3.gz"),
"md5.txt"=file.path(.gitHubURL,"md5.txt"),
"202_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"202_subset_sortmerna_trimmomatic_sorted.bam"),
"207_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"207_subset_sortmerna_trimmomatic_sorted.bam"),
"213.1_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"213.1_subset_sortmerna_trimmomatic_sorted.bam"),
"221_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"221_subset_sortmerna_trimmomatic_sorted.bam"),
"226.1_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"226.1_subset_sortmerna_trimmomatic_sorted.bam"),
"229.1_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"229.1_subset_sortmerna_trimmomatic_sorted.bam"),
"202_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"202_subset_sortmerna_trimmomatic_sorted.bam.bai"),
"207_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"207_subset_sortmerna_trimmomatic_sorted.bam.bai"),
"213.1_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"213.1_subset_sortmerna_trimmomatic_sorted.bam.bai"),
"221_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"221_subset_sortmerna_trimmomatic_sorted.bam.bai"),
"226.1_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"226.1_subset_sortmerna_trimmomatic_sorted.bam.bai"),
"229.1_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"229.1_subset_sortmerna_trimmomatic_sorted.bam.bai")),
envir=as.environment("package:easyRNASeq"))
}
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# to re-build the documentation and namespace
# library(roxygen2)
# roxygenize("../easyrnaseq-devel/",roclets=c('rd', 'collate', 'namespace'),clean=TRUE)
# to update the package versions
# pkg <- c("Biobase","BiocGenerics","BiocParallel","biomaRt","Biostrings",
# "DESeq","edgeR","GenomeInfoDb","genomeIntervals",
# "GenomicAlignments","GenomicRanges","SummarizedExperiment",
# "IRanges","LSD","Rsamtools","S4Vectors","ShortRead",
# "BiocStyle","rappdirs,
# "BSgenome",
# "BSgenome.Dmelanogaster.UCSC.dm3","GenomicFeatures",
# "RUnit")
# pkg[! pkg %in% rownames(installed.packages())]
# installed.packages()[pkg,"Version"]
##==========================
## package details
##==========================
#' Count summarization and normalization pipeline for Next Generation Sequencing data.
#'
#' Offers functionalities to summarize read counts per feature of interest, e.g. exons, transcripts, genes, etc.
#' Offers functionalities to normalize the summarized counts using 3rd party packages like \code{\link[DESeq:newCountDataSet]{DESeq}}
#' or \code{\link[edgeR:DGEList]{edgeR}}.
#'
#' @section Methods:
#' The main function \code{\link[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}} will summarize the counts per
#' feature of interest, for as many samples as provided and will return a
#' count matrix (N*M) where N are the features and M the samples.
#' This data can be corrected to \pkg{RPKM} in which case
#' a matrix of corrected value is returned instead, with the same dimensions.
#' Alternatively a \code{\linkS4class{RangedSummarizedExperiment}} can be returned and this
#' is expected to be the default in the upcoming version of easyRNASeq (as of 1.5.x).
#' If the necessary sample
#' information are provided, the data can be normalized using either \code{\link[DESeq:newCountDataSet]{DESeq}}
#' or \code{\link[edgeR:DGEList]{edgeR}} and the corresponding package object returned.
#' For more insider details, and step by step functions, see:
#' \tabular{ll}{
#' \code{\link[easyRNASeq:ShortRead-methods]{ShortRead methods}} for pre-processing the data.
#' \code{\link[easyRNASeq:easyRNASeq-annotation-methods]{easyRNASeq annotation methods}} for getting the annotation.
#' \code{\link[easyRNASeq:easyRNASeq-coverage-methods]{easyRNASeq coverage methods}} for computing the coverage from a Short Read Alignment file.
#' \code{\link[easyRNASeq:easyRNASeq-summarization-methods]{easyRNASeq summarization methods}} for summarizing the data.
#' \code{\link[easyRNASeq:easyRNASeq-correction-methods]{easyRNASeq correction methods}} for correcting the data (i.e. generating RPKM).
#' \code{\link[easyRNASeq:edgeR-methods]{edgeR methods}} for post-processing the data.
#' \code{\link[easyRNASeq:DESeq-methods]{DESeq methods}} for post-processing the data.
#' }
#'
#' @name easyRNASeq package
#' @rdname easyRNASeq-package
#' @aliases easyRNASeq-package assay type BamFileList BamFileList-class IRanges
#' GRanges-class GRanges SRFilterResult SummarizedExperiment RangedSummarizedExperiment-class
#' chromosomeFilter compose nFilter
#' @docType package
#' @author Nicolas Delhomme, Bastian Schiffthaler, Ismael Padioleau
#' @keywords package
#' @seealso
#' The class RNAseq specification:
#' \code{\linkS4class{RNAseq}}
#'
#' The default output class specification:
#' \code{\linkS4class{RangedSummarizedExperiment}}
#'
#' The imported packages:
#' \code{\link[biomaRt:useMart]{biomaRt}}
#' \code{\link[BiocParallel:BiocParallel-package]{BiocParallel}}
#' \code{\link[edgeR:DGEList]{edgeR}}
#' \code{\link[genomeIntervals:Genome_intervals_stranded-class]{genomeIntervals}}
#' \code{\link[Biostrings:XString-class]{Biostrings}}
#' \code{\link[BSgenome:BSgenome-class]{BSgenome}}
#' \code{\link[DESeq:newCountDataSet]{DESeq}}
#' \code{\link[GenomicRanges:GRanges-class]{GenomicRanges}}
#' \code{\link[IRanges:IRanges-constructor]{IRanges}}
#' \code{\link[Rsamtools:scanBam]{Rsamtools}}
#' \code{\link[ShortRead:readAligned]{ShortRead}}
#'
#' The suggested packages:
#' \code{\link[parallel:makeCluster]{parallel}}
#' \code{\link[GenomicFeatures:TxDb-class]{GenomicFeatures}}
#'
#' The following classes and functions that are made available from
#' other packages:
#' \itemize{
#' \item{Classes}{
#' \code{\link[Rsamtools:BamFile-class]{BamFileList-class}}
#' \code{\linkS4class{CountDataSet}}
#' \code{\linkS4class{RangedSummarizedExperiment}}
#' }
#' \item{Functions/Methods}{
#' \code{\link[DESeq:estimateDispersions]{DESeq estimate size factor and
#' estimate dispersion functions}}
#' \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{
#' The RangedSummarizedExperiment assay accessor}
#' }
#' The locfit function \code{\link[locfit]{locfit}}
#' The BamFileList constructor \code{\link[Rsamtools:BamFile-class]{BamFileList-class}}
#' The IRanges constructor \code{\link[IRanges]{IRanges-constructor}}
#' For the SRFilterResult,
#' chromosomeFilter, compose and nFilter methods\code{\link[ShortRead]{srFilter}}
#' }
#' }
#'
#' @examples
#' # the data
#' tdir <- tutorialData()
#'
#' # get the example annotation file - we retrieve a gtf file from GitHub
#' annot <- fetchData("Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz")
#'
#' # create the AnnotParam
#' annotParam <- AnnotParam(
#' datasource=annot,
#' type="gtf")
#'
#' # create the synthetic transcripts
#' annotParam <- createSyntheticTranscripts(annotParam,verbose=FALSE)
#'
#' # create the RnaSeqParam
#' rnaSeqParam <- RnaSeqParam(annotParam=annotParam,countBy="gene")
#'
#' # get the bamfiles (from the Bioc cache in this example)
#' filenames <- dir(tdir,pattern="[A,T].*\\.bam$",full.names=TRUE)
#' indexnames <- sapply(paste0(sub(".*_","",basename(filenames)),".bai"),fetchData)
#' bamFiles <- getBamFileList(filenames,indexnames)
#'
#' # get a RangedSummarizedExperiment containing the counts table
#' sexp <- simpleRNASeq(
#' bamFiles=bamFiles,
#' param=rnaSeqParam,
#' verbose=TRUE
#' )
#'
#' # get the counts
#' assays(sexp)$genes
#'
#'
NULL
##==========================
# To define the NAMESPACE
##==========================
# library(codetoolsBioC)
# library(easyRNASeq)
# writeNamespaceImports("easyRNASeq")
# import classes
#' @importClassesFrom Biostrings DNAStringSet
#' @importClassesFrom DESeq CountDataSet
#' @importClassesFrom edgeR DGEList
#' @importClassesFrom genomeIntervals Genome_intervals Genome_intervals_stranded
#' @importClassesFrom GenomicAlignments GAlignments GAlignmentPairs
#' @importClassesFrom GenomicRanges GRanges GRangesList
#' @importClassesFrom SummarizedExperiment RangedSummarizedExperiment
#' @importClassesFrom IRanges RleList
#' @importClassesFrom S4Vectors Annotated Vector DataFrame SimpleList
#' @importClassesFrom methods ANY character "function" integer
#' list matrix missing numeric vector
#' @importClassesFrom Rsamtools BamFile BamFileList
#' @importClassesFrom ShortRead AlignedRead ShortReadQ
# import S4 methods
#' @importMethodsFrom Biobase fData varMetadata
#' @importFrom BiocFileCache bfcadd bfcdownload bfcneedsupdate bfcquery bfcrpath
#' @importMethodsFrom BiocGenerics annotation cbind clusterApply
#' colnames counts duplicated estimateDispersions estimateSizeFactors
#' eval fileName get intersect lapply match order path paste pmax rbind
#' rownames sapply strand "strand<-" table unique
#' @importMethodsFrom Biostrings type
#' @importMethodsFrom DESeq estimateSizeFactors estimateDispersions
#' @importMethodsFrom genomeIntervals readGff3 writeGff3
#' @importMethodsFrom GenomeInfoDb seqinfo seqlengths "seqlengths<-"
#' seqlevels "seqlevels<-" seqnames "seqnames<-"
#' @importMethodsFrom GenomicAlignments cigar summarizeOverlaps
#' @importMethodsFrom GenomicRanges grglist
#' @importMethodsFrom IRanges as.list as.matrix
#' "colnames<-" countOverlaps coverage end "end<-" findOverlaps
#' gsub mean median narrow nchar ranges reduce "rownames<-" space
#' start "start<-" sub tolower unlist values which width
#' @importMethodsFrom methods coerce initialize show
#' @importMethodsFrom Rsamtools asMates "asMates<-" countBam scanBam
#' scanBamHeader ScanBamParam yieldSize "yieldSize<-"
#' @importMethodsFrom S4Vectors "%in%" as.table elementMetadata
#' "elementMetadata<-" elementNROWS levels mcols metadata
#' "metadata<-" Rle runLength runsum runValue split substr
#' @importMethodsFrom ShortRead chromosome id position readAligned
#' srdistance sread srFilter writeFastq
#' @importMethodsFrom SummarizedExperiment assay assays "assays<-"
#' colData "colData<-" rowRanges "rowRanges<-"
# import methods
#' @importFrom biomaRt getBM listDatasets useDataset useMart
#' @importFrom BiocParallel MulticoreParam SerialParam
#' @importFrom Biostrings DNAStringSet
#' @importFrom DESeq fitInfo newCountDataSet
#' @importFrom edgeR calcNormFactors DGEList estimateCommonDisp
#' estimateTagwiseDisp maPlot plotMDS.DGEList plotMeanVar plotBCV
#' @importFrom genomeIntervals getGffAttribute parseGffAttributes
#' @importFrom GenomicAlignments GAlignments readGAlignments readGAlignmentPairs
#' @importFrom GenomicRanges GRanges GRangesList
#' @importFrom graphics abline axis axTicks boxplot grid hist legend lines
#' mtext par plot rect
#' @importFrom IRanges IRanges IRangesList LogicalList
#' SplitDataFrameList RleList
#' @importFrom locfit locfit lp
#' @importFrom LSD heatscatter
#' @importFrom methods as extends is new
#' @importFrom parallel makePSOCKcluster parLapply stopCluster
#' @importFrom rappdirs user_cache_dir
#' @importFrom Rsamtools BamFileList bamFlagTest index scanBamFlag
#' @importFrom S4Vectors endoapply DataFrame queryHits SimpleList
#' @importFrom ShortRead alignData chromosomeFilter compose nFilter
#' SRFilterResult
#' @importFrom stats aggregate na.omit
#' @importFrom SummarizedExperiment SummarizedExperiment
#' @importFrom utils combn str packageVersion
# and export!
#' @exportClass BamFileList GRanges RangedSummarizedExperiment
#' @exportMethod assay assays colData estimateDispersions estimateSizeFactors fileName metadata rowRanges seqinfo seqlengths seqlevels "seqlevels<-" seqnames "seqnames<-" split srFilter width writeFastq writeGff3
#' @export alignData basename chromosomeFilter compose BamFileList GRanges IRanges locfit lp newCountDataSet nFilter readAligned SRFilterResult SummarizedExperiment
NULL
##==========================
# To detail the deprecation
##==========================
# nothing at the time - copy the defunct block if needed and
# replace defunct by deprecated
##==========================
# To detail defunct function
##==========================
#' The following function are defunct:
#' \itemize{
#' \item \code{\link[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}}
#' \item \code{\link[easyRNASeq:easyRNASeq-coverage-methods]{fetchCoverage}}
#' \item \code{fetchAnnotation}
#' \item \code{knownOrganisms}
#' \item \code{plotDispersionEstimates,DGEList-method}
#' }
#'
#' \itemize{
#' \item The \code{plotDispersionEstimates,DGEList-method}
#' function is superseded by the \code{\link[edgeR:plotBCV]{plotBCV}} function
#' as the \pkg{edgeR} DGEList object structure changed
#' \item The \code{\link[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}} function is superseded by the
#' \code{\link[easyRNASeq:easyRNASeq-simpleRNASeq]{simpleRNASeq}} function to consolidate and
#' prune the overall package. The changes are based on user comments and on the
#' general standardization occuring in the field.
#' \item The \code{\link[easyRNASeq:easyRNASeq-coverage-methods]{fetchCoverage}} function only had two
#' parameters deprecated as the consequence of the package consolidation. As the scanBam
#' function is not called directly anymore but through higher level functions (from the
#' GenomicRanges package), the 'what' and 'isUnmappedQuery' parameters were obsolete.
#' }
#' @aliases plotDispersionEstimates,DGEList-method fetchAnnotation knownOrganisms
#' easyRNASeq easyRNASeq,RNAseq-method fetchCoverage,RNAseq-method fetchCoverage
#' organismName<- organismName organismName,RNAseq-method organismName<-,RNAseq-method
#' @name Defunct functions
#' @rdname easyRNASeq-defunct
NULL
##==========================
# To detail dataset
##==========================
#' Dataset included in the package
#'
#' The package contains a dataset from the \emph{Robinson, Delhomme et al., 2014}
#' publication.
#' \itemize{
#' \item{RobinsonDelhomme2014}{a normalised expression count table. This dataset was
#' generated from 17 \emph{Populus tremula} - Eurasian
#' aspen - trees used to assess the sexual dimorphism of this dioecious species. This
#' count matrix has been generating following published pre-processing
#' guidelines - see \url{http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis} -
#' and the resulting HTSeq files have been collated and the obtained raw count
#' matrix submitted to a variance stabilising transformation. Subsequently, the
#' values have been transformed so that the minimal vst values - that
#' corresponds to an absence of expression - is 0. Hence the counts in the
#' matrix are library-size normalized, variance stabilised expression values,
#' with a minimal value of 0.}
#' }
#' @aliases easyRNASeq-datasets
#' RobinsonDelhomme2014
#' @name easyRNASeq-datasets
#' @rdname easyRNASeq-datasets
#' @keywords data
NULL
##==========================
# To detail hardcoded parameters
##==========================
#' Objects created when the package is attached.
#'
#' The package creates the following objects when attached
#' \itemize{
#' \item GTF.FIELDS
#' \item ANNOTATION.TYPE
#' \item TUTORIAL.DATA
#' \item VIGNETTE.DATA
#' }
#'
#' These objects hold the following information
#' \itemize{
#' \item GTF.FIELDS \code{c("gene_id","transcript_id","exon_id","gene_name")}
#' \item ANNOTATION.TYPE \code{c(mRNA="mRNA",exon="exon")}
#' \item TUTORIAL.DATA: The list of files needed for the help and test
#' pages
#' \item VIGNETTE.DATA: The list of files needed for the vignette
#' }
#' and are designed as global variables to expose the
#' fact that they are hardcoded. These exist as
#' placeholder in case a user would require different
#' values for these.
#'
#' @aliases easyRNASeq-global-variables .onAttach ANNOTATION.TYPE GTF.FIELDS
#' TUTORIAL.DATA VIGNETTE.DATA
#' @name easyRNASeq-global-variables
#' @rdname easyRNASeq-global-variables
#' @param libname a character string giving the library directory where the package defining the namespace was found.
#' @param pkgname a character string giving the name of the package.
#' @seealso \code{\link[base:ns-hooks]{.onAttach}} in the \code{base} package.
#' @keywords internal
globalVariables("GTF.FIELDS")
globalVariables("ANNOTATION.TYPE")
globalVariables("TUTORIAL.DATA")
globalVariables("VIGNETTE.DATA")
".onAttach" <- function(libname,pkgname){
assign("GTF.FIELDS",c("gene_id","transcript_id","exon_id",
"gene_name"),
envir=as.environment("package:easyRNASeq"))
assign("ANNOTATION.TYPE",c(mRNA="mRNA",exon="exon"),
envir=as.environment("package:easyRNASeq"))
.gitHubURL <- "https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq"
assign("TUTORIAL.DATA",
c(ACACTG.bam=file.path(.gitHubURL,"ACACTG.bam"),
ACTAGC.bam=file.path(.gitHubURL,"ACTAGC.bam"),
ATGGCT.bam=file.path(.gitHubURL,"ATGGCT.bam"),
TTGCGA.bam=file.path(.gitHubURL,"TTGCGA.bam"),
ACACTG.bam.bai=file.path(.gitHubURL,"ACACTG.bam.bai"),
ACTAGC.bam.bai=file.path(.gitHubURL,"ACTAGC.bam.bai"),
ATGGCT.bam.bai=file.path(.gitHubURL,"ATGGCT.bam.bai"),
TTGCGA.bam.bai=file.path(.gitHubURL,"TTGCGA.bam.bai"),
"Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz"=
file.path(.gitHubURL,"Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz"),
gAnnot.rda=file.path(.gitHubURL,"gAnnot.rda"),
"Dmel-mRNA-exon-r5.52.gff3.gz"=file.path(.gitHubURL,"Dmel-mRNA-exon-r5.52.gff3.gz")),
envir=as.environment("package:easyRNASeq"))
assign("VIGNETTE.DATA",
c("Ptrichocarpa_210_v3.0_gene_exons.gff3.gz"=
file.path(.gitHubURL,"Ptrichocarpa_210_v3.0_gene_exons.gff3.gz"),
"md5.txt"=file.path(.gitHubURL,"md5.txt"),
"202_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"202_subset_sortmerna_trimmomatic_sorted.bam"),
"207_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"207_subset_sortmerna_trimmomatic_sorted.bam"),
"213.1_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"213.1_subset_sortmerna_trimmomatic_sorted.bam"),
"221_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"221_subset_sortmerna_trimmomatic_sorted.bam"),
"226.1_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"226.1_subset_sortmerna_trimmomatic_sorted.bam"),
"229.1_subset_sortmerna_trimmomatic_sorted.bam"=
file.path(.gitHubURL,"229.1_subset_sortmerna_trimmomatic_sorted.bam"),
"202_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"202_subset_sortmerna_trimmomatic_sorted.bam.bai"),
"207_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"207_subset_sortmerna_trimmomatic_sorted.bam.bai"),
"213.1_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"213.1_subset_sortmerna_trimmomatic_sorted.bam.bai"),
"221_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"221_subset_sortmerna_trimmomatic_sorted.bam.bai"),
"226.1_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"226.1_subset_sortmerna_trimmomatic_sorted.bam.bai"),
"229.1_subset_sortmerna_trimmomatic_sorted.bam.bai"=
file.path(.gitHubURL,"229.1_subset_sortmerna_trimmomatic_sorted.bam.bai")),
envir=as.environment("package:easyRNASeq"))
}
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