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)
}