enrichPeakOverlap: enrichPeakOverlap

Description Usage Arguments Value Author(s)

View source: R/enrichOverlap.R

Description

calculate overlap significant of ChIP experiments based on the genome coordinations

Usage

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enrichPeakOverlap(queryPeak, targetPeak, TxDb = NULL,
  pAdjustMethod = "BH", nShuffle = 1000, chainFile = NULL,
  pool = TRUE, mc.cores = detectCores() - 1, verbose = TRUE)

Arguments

queryPeak

query bed file or GRanges object

targetPeak

target bed file(s) or folder that containing bed files or a list of GRanges objects

TxDb

TxDb

pAdjustMethod

pvalue adjustment method

nShuffle

shuffle numbers

chainFile

chain file for liftOver

pool

logical, whether pool target peaks

mc.cores

number of cores, see mclapply

verbose

logical

Value

data.frame

Author(s)

G Yu


ChIPseeker documentation built on Nov. 1, 2018, 2:04 a.m.