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(),
  oprefix = 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. Regions with signals lower than cutoff will not be considerred as enriched regions. 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
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	Output file name. Mutually exclusive with –o-prefix
oprefix	The PREFIX of output bedGraph file to write scores. If it is given as A, and method is 'ppois', output file will be A_ppois.bdg. Mutually exclusive with -o/–ofile.
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 Sept. 24, 2024, 11:09 p.m.