enrichPeakOverlap: enrichPeakOverlap

In YuLab-SMU/ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

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

YuLab-SMU/ChIPseeker documentation built on Feb. 11, 2024, 5:22 p.m.