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R
ChIPseeker

enrichPeakOverlap

enrichPeakOverlap

Description

calculate overlap significant of ChIP experiments based on the genome coordinations

Usage

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

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

v1.26.2
Artistic-2.0
Authors
Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>), Yun Yan [ctb], Hervé Pagès [ctb], Michael Kluge [ctb], Thomas Schwarzl [ctb], Zhougeng Xu [ctb]
Initial release

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