enrichPeakOverlap {ChIPseeker} | R Documentation

## 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

[Package ChIPseeker version 1.30.3 Index]