Wrapper function for Homer's makeTagDirectory and findPeaks

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

Kathryn Rozen-Gagnon

Examples

if (FALSE) {
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)
}