bdgopt: bdgopt

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

bdgopt

Description

Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS3 are accpetable.

Usage

bdgopt(
  ifile,
  method = c("multiply", "add", "p2q", "max", "min"),
  extraparam = numeric(),
  outputfile = character(),
  outdir = ".",
  log = TRUE,
  verbose = 2L
)

Arguments

ifile	MACS score in bedGraph. Note: this must be a bedGraph file covering the ENTIRE genome. REQUIRED
method	Method to modify the score column of bedGraph file. Available choices are: multiply, add, max, min, or p2q. 1) multiply, the EXTRAPARAM is required and will be multiplied to the score column. If you intend to divide the score column by X, use value of 1/X as EXTRAPARAM. 2) add, the EXTRAPARAM is required and will be added to the score column. If you intend to subtract the score column by X, use value of -X as EXTRAPARAM. 3) max, the EXTRAPARAM is required and will take the maximum value between score and the EXTRAPARAM. 4) min, the EXTRAPARAM is required and will take the minimum value between score and the EXTRAPARAM. 5) p2q, this will convert p-value scores to q-value scores using Benjamini-Hochberg process. The EXTRAPARAM is not required. This method assumes the scores are -log10 p-value from MACS3. Any other types of score will cause unexpected errors. Default="p2q"
extraparam	The extra parameter for METHOD. Check the detail of -m option.
outputfile	Output BEDGraph filename. Required.
outdir	The output directory.
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"]]
c1 <- callpeak(CHIP, CTRL, gsize = 5.2e7, cutoff_analysis = TRUE,
               outdir = tempdir(), name = "callpeak_narrow0",
               store_bdg = TRUE)
cfile <- grep("treat_pileup.bdg", c1$outputs, value = TRUE)
bdgopt(cfile, method = "min", extraparam = 10,
       outdir = tempdir(), outputfile = "bdgopt_min.bdg")

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