ctk_tag2collapse: Wrapper function for ctk's tag2collapse

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Wrapper function for ctk's tag2collapse

Description

Wrapper function for ctk's tag2collapse

Usage

ctk_tag2collapse(
  filesToRun,
  outFile = file.path(dirname(filesToRun), paste0("TC_", basename(filesToRun))),
  sb = "tag2collapse.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  keepMaxScore = TRUE,
  keepTagName = TRUE,
  weight = TRUE,
  bigFile = FALSE,
  weightInName = TRUE,
  randomBarcode = TRUE,
  seqErrorModel = "em-local",
  outputSeqError = NULL,
  em = NULL,
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_tag2collapse_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_tag2collapse_stdout.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE,
  writelog = T
)

Arguments

filesToRun	path to file to process (BED).
outFile	path to output file
sb	path to tag2collapse.pl from CTK.
perl	path to PERL.
PATHTOPERLLIB	path to PERL5LIB.
keepMaxScore	keep the tag with the most weight (instead of the longest one) as representative.
keepTagName	do not change tag name (no extra information).
weight	consider the weight of each tag.
bigFile	Set to TRUE when files are big.
weightInName	find weight in name.
randomBarcode	random barcode exists, no collapse for different barcodes.
seqErrorModel	sequencing error model to use, "alignment" or "em-local" (default) or "em-global" or "fix=0.01".
outputSeqError	output sequencing errors estimated by the EM algorithm.
em	EM threshold to infer reliability of each collapsed read (when have random linker, -1=no EM).
stderr	path to stdout file.
stdout	path to stdout file.
useClipRConda	use conda environment installed by Herper, TRUE (default) or FALSE.
additional_Args	Additional arguments to be passed to system call.
verbose	print messages, TRUE or FALSE (default).
writelog	write stderr/stdout logs, TRUE (default) or FALSE

Value

path to collapsed BED file.

Author(s)

Kathryn Rozen-Gagnon

Examples

testFasta <- system.file("extdata/hg19Small.fa",package="CLIPflexR")
myIndex <-suppressWarnings(bowtie2_index(testFasta, overwrite = TRUE))
testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")
FqFile_FF <- ctk_fastqFilter(testFQ,qsFilter="mean:0-29:20",verbose=TRUE)
FqFile <- decompress(FqFile_FF,overwrite=TRUE)
FqFile_clipped <- fastx_clipper(FqFile,length=20)
FqFile_QF <- fastq_quality_trimmer(FqFile_clipped)
FqFile_Col <- ctk_fastq2collapse(FqFile_QF,verbose=TRUE)
FqFile_QFColStripped <- ctk_stripBarcode(FqFile_Col,linkerlength=5,inputFormat="fastq")
bam <- suppressWarnings(bowtie_align(FqFile_QFColStripped,myIndex, 
overwrite=TRUE, inputFormat="fastq"))
parsedAlignment <- ctk_parseAlignment(bam)
ctk_tag2collapse(parsedAlignment,weight=FALSE,randomBarcode=FALSE,
weightInName = FALSE,verbose = TRUE)

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.