bdgbroadcall: bdgbroadcall

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

bdgbroadcall

Description

Call broad 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

bdgbroadcall(
  ifile,
  cutoffpeak = 2,
  cutofflink = 1,
  minlen = 200L,
  lvl1maxgap = 30L,
  lvl2maxgap = 800L,
  trackline = TRUE,
  outdir = ".",
  outputfile = character(),
  log = TRUE,
  verbose = 2L
)

Arguments

ifile	MACS score in bedGraph. REQUIRED.
cutoffpeak	Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS3, score 2 means qvalue 0.01. DEFAULT: 2
cutofflink	Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS3, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. DEFAULT: 1", default = 1
minlen	minimum length of peak, better to set it as d value. DEFAULT: 200", default = 200
lvl1maxgap	maximum gap between significant peaks, better to set it as tag size. DEFAULT: 30
lvl2maxgap	maximum linking between significant peaks, better to set it as 4 times of d value. DEFAULT: 800
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")
bdgbroadcall(c1$outputs, cutoffpeak = 2, cutofflink = 1.5,
             outdir = tempdir(), outputfile = "bdgbroadcall")

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