bdgpeakcall: bdgpeakcall

In macs3-project/MACSr: MACS: Model-based Analysis for ChIP-Seq

bdgpeakcall

Description

Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS3 are accpetable.

Usage

bdgpeakcall(
  ifile,
  cutoff = 5,
  minlen = 200L,
  maxgap = 30L,
  call_summits = FALSE,
  cutoff_analysis = FALSE,
  trackline = TRUE,
  outdir = ".",
  outputfile = character(),
  log = TRUE,
  verbose = 2L
)

Arguments

ifile	MACS score in bedGraph. REQUIRED.
cutoff	Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS3, score 5 means pvalue 1e-5. DEFAULT: 5", default = 5.
minlen	minimum length of peak, better to set it as d value. DEFAULT: 200", default = 200.
maxgap	maximum gap between significant points in a peak, better to set it as tag size. DEFAULT: 30", default = 30.
call_summits	If set, MACS will use a more sophisticated approach to find all summits in each enriched peak region DEFAULT: False",default=False.
cutoff_analysis	While set, bdgpeakcall will analyze number or total length of peaks that can be called by different cutoff then output a summary table to help user decide a better cutoff. Note, minlen and maxgap may affect the results. DEFAULT: False", default = False.
trackline	Tells MACS not to include trackline with bedGraph files. The trackline is required by UCSC.
outdir	The output directory.
outputfile	The output file.
log	Whether to capture logs.
verbose	Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT:2

Value

macsList object.

Examples

eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
CTRL <- eh[["EH4563"]]
p1 <- pileup(CHIP, outdir = tempdir(),
             outputfile = "pileup_ChIP_bed.bdg", format = "BED")
p2 <- pileup(CTRL, outdir = tempdir(),
             outputfile = "pileup_CTRL_bed.bdg", format = "BED")
c1 <- bdgcmp(p1$outputs, p2$outputs, outdir = tempdir(),
             oprefix = "bdgcmp", pseudocount = 1, method = "FE")
bdgpeakcall(c1$outputs, cutoff = 2,
            outdir = tempdir(), outputfile = "bdgpeakcall")

macs3-project/MACSr documentation built on Nov. 24, 2023, 12:47 p.m.