cmbreps

Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS3 are accpetable.

cmbreps(
  ifiles = list(),
  method = c("fisher", "max", "mean"),
  outputfile = character(),
  outdir = ".",
  log = TRUE,
  verbose = 2L
)

Arguments

ifiles

MACS score in bedGraph for each replicate. Require at least 2 files such as '-i A B C D'. REQUIRED

method

to use while combining scores from replicates. 1) fisher: Fisher's combined probability test. It requires scores in ppois form (-log10 pvalues) from bdgcmp. Other types of scores for this method may cause cmbreps unexpected errors. 2) max: take the maximum value from replicates for each genomic position. 3) mean: take the average value. Note, except for Fisher's method, max or mean will take scores AS IS which means they won't convert scores from log scale to linear scale or vice versa.", default="fisher"

outputfile

Output BEDGraph filename for combined scores.

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"]]
#> see ?MACSdata and browseVignettes('MACSdata') for documentation
#> loading from cache
CTRL <- eh[["EH4563"]]
#> see ?MACSdata and browseVignettes('MACSdata') for documentation
#> loading from cache
c1 <- callpeak(CHIP, CTRL, gsize = 5.2e7, cutoff_analysis = TRUE,
               outdir = tempdir(), name = "callpeak_narrow0",
               store_bdg = TRUE)
#> 
cmbreps(ifiles = list(c1$outputs[1], c1$outputs[7]),
        method = "max", outdir = tempdir(), outputfile = "cmbreps")
#> 
#> macsList class
#> $outputs:
#>  /tmp/RtmpkYWDbh/cmbreps 
#> $arguments: ifiles, method, outputfile, outdir 
#> $log:
#>