bdgcmp: bdgcmp

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

bdgcmp

Description

Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS3 are accpetable.

Usage

bdgcmp(
  tfile,
  cfile,
  sfactor = 1,
  pseudocount = 0,
  method = c("ppois", "qpois", "subtract", "logFE", "FE", "logLR", "slogLR", "max"),
  oprefix = character(),
  outputfile = list(),
  outdir = ".",
  log = TRUE,
  verbose = 2L
)

Arguments

tfile	Treatment bedGraph file, e.g. *_treat_pileup.bdg from MACSv2. REQUIRED
cfile	Control bedGraph file, e.g. *_control_lambda.bdg from MACSv2. REQUIRED
sfactor	Scaling factor for treatment and control track. Keep it as 1.0 or default in most cases. Set it ONLY while you have SPMR output from MACS3 callpeak, and plan to calculate scores as MACS3 callpeak module. If you want to simulate 'callpeak' w/o '–to-large', calculate effective smaller sample size after filtering redudant reads in million (e.g., put 31.415926 if effective reads are 31,415,926) and input it for '-S'; for 'callpeak –to-large', calculate effective reads in larger sample. DEFAULT: 1.0
pseudocount	The pseudocount used for calculating logLR, logFE or FE. The count will be applied after normalization of sequencing depth. DEFAULT: 0.0, no pseudocount is applied.
method	Method to use while calculating a score in any bin by comparing treatment value and control value. Available choices are: ppois, qpois, subtract, logFE, FE, logLR, slogLR, and max. They represent Poisson Pvalue (-log10(pvalue) form) using control as lambda and treatment as observation, q-value through a BH process for poisson pvalues, subtraction from treatment, linear scale fold enrichment, log10 fold enrichment(need to set pseudocount), log10 likelihood between ChIP-enriched model and open chromatin model(need to set pseudocount), symmetric log10 likelihood between two ChIP-enrichment models, or maximum value between the two tracks. Default option is ppois.
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.
outputfile	Output filename. Mutually exclusive with –o-prefix. The number and the order of arguments for –ofile must be the same as for -m.
outdir	The output directory.
log	Whether to capture logs.
verbose	Set verbose level. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. If you want to know where are the duplicate reads, use 3. 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")

macs3-project/MACSr documentation built on Sept. 24, 2024, 11:09 p.m.