homer_peaks: Wrapper function for Homer's makeTagDirectory and findPeaks
In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

homer_peaks

R Documentation

Wrapper function for Homer's makeTagDirectory and findPeaks

Description

Wrapper function for Homer's makeTagDirectory and findPeaks

Usage

homer_peaks(
  fileTofqs,
  maketagdir = "makeTagDirectory",
  findpeaks = "findPeaks",
  format = "bed",
  createSingleTagsTSV = TRUE,
  tagdir = file.path(dirname(fileTofqs), gsub("\\.bed", "",
    make.names(basename(fileTofqs)))),
  style = "factor",
  foldEnrichmentOverLocal = 2,
  localSize = 10000,
  strand = "seperate",
  minDist = 50,
  size = 10,
  fragLength = 10,
  genomeSize = NULL,
  stderr = file.path(dirname(fileTofqs), paste0(basename(fileTofqs),
    "_homer_stderr.txt")),
  stdout = file.path(dirname(fileTofqs), paste0(basename(fileTofqs),
    "_homer_stderr.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE,
  writelog = T
)

Arguments

`fileTofqs`	path to file to process (BED).
`maketagdir`	path to makeTagDirectory from Homer toolkit.
`findpeaks`	path to findpeaks from Homer toolkit.
`format`	input format, "bed" (default).
`createSingleTagsTSV`	create a single tags.tsv file for all "chromosomes".
`tagdir`	name of Tag Directory.
`style`	type of Homer peak calling, "factor", "histone", "groseq", "tss", "dnase", "super" or "mCs".
`foldEnrichmentOverLocal`	fold enrichment over local tag count.
`localSize`	region to check for local tag enrichment.
`strand`	find peaks using tags on "both" or "separate" (default) strands.
`minDist`	minimum distance between peaks.
`size`	peak size.
`fragLength`	approximate fragment length.
`genomeSize`	genome size, default is NULL (2E9, applicable for human or mouse), set integer to specify for your genome.
`stderr`	path to stderr 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 unzipped file

Author(s)

Kathryn Rozen-Gagnon

Examples

## Not run: 
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 <- decompress(testFQ,overwrite = TRUE)
FqFile_QF <- fastq_quality_filter(FqFile)
FqFile_QFCollapsed <- fastx_collapser(FqFile_QF)
FqFile_QFColStripped <- ctk_stripBarcode(FqFile_QFCollapsed)
FqFile_QFColStpClipped <- fastx_clipper(FqFile_QFColStripped)
bam <- suppressWarnings(bowtie_align(FqFile_QFColStpClipped,myIndex, overwrite = TRUE))
bed <- bamtobed(bam)
homer_peaks(bed)

## End(Not run)

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