ctk_tag2peak: Wrapper function for ctk's bed2rgb
In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

ctk_tag2peak

R Documentation

Wrapper function for ctk's bed2rgb

Description

Wrapper function for ctk's bed2rgb

Usage

ctk_tag2peak(
  filesToRun,
  outFile = paste0(file_path_sans_ext(filesToRun), ".peak.bed"),
  outBoundary = paste0(file_path_sans_ext(filesToRun), ".boundary.bed"),
  outHalfPH = paste0(file_path_sans_ext(filesToRun), ".halfPF.bed"),
  sb = "tag2peak.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  bigFile = FALSE,
  ss = TRUE,
  valleySeeking = TRUE,
  valleyDepth = 0.9,
  genes = NULL,
  multiTest = FALSE,
  useExpr = FALSE,
  skipOutOfRangePeaks = FALSE,
  pCutOff = 0.01,
  minPH = 2,
  maxPH = -1,
  gap = -1,
  peakPrefix = "Peak",
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_tag2peak_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_tag2peak_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 (BED).
`outBoundary`	output cluster boundaries.
`outHalfPH`	output half peak height boundaries.
`sb`	path to tag2peak.pl from CTK.
`perl`	path to PERL.
`PATHTOPERLLIB`	path to PERL5LIB.
`bigFile`	big input file, TRUE or FALSE (default).
`ss`	separate the two strands, TRUE (default) or FALSE.
`valleySeeking`	find candidate peaks by valley seeking.
`valleyDepth`	depth of valley if valley seeking (between 0.5 and 1, default is 0.9).
`genes`	custom gene bed file for scan statistics (will override –dbkey)
`multiTest`	do Bonferroni multiple test correction.
`useExpr`	use expression levels given in the score column in the gene bed file for normalization.
`skipOutOfRangePeaks`	Remove out of bounds ranges.
`pCutOff`	threshold of p-value to call peak (e.g. 0.01).
`minPH`	min peak height.
`maxPH`	max peak height.
`gap`	merge cluster peaks closer than the gap (-1, no merge if < 0).
`peakPrefix`	prefix of peak id (Peak) (so output file will look like Peak1, Peak2, etc).
`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 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)
myCollaped <- ctk_tag2collapse(parsedAlignment,weight=FALSE,randomBarcode=FALSE,
weightInName=FALSE,verbose=TRUE)
myrgbBed <- ctk_bed2rgb(myCollaped,col="128,0,0")
ctk_tag2profile(myrgbBed,verbose=TRUE)

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