bdp: obtain the peaks near bi-directional promoters

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

obtain the peaks near bi-directional promoters

Description

Obtain the peaks near bi-directional promoters. Also output percent of peaks near bi-directional promoters.

Usage

bdp(peaks, annoData, maxgap = 2000L, ...)

Arguments

peaks	peak list, GRanges object
annoData	annotation data, annoGR object
maxgap	maxgap between peak and TSS
...	Not used.

Value

Output is a list of GRanges object of the peaks near bi-directional promoters.

Author(s)

Jianhong Ou

See Also

See Also as annoPeaks, annoGR

Examples

  if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library(ensembldb)
    library(EnsDb.Hsapiens.v75)
    data("myPeakList")
    annoGR <- annoGR(EnsDb.Hsapiens.v75)
    seqlevelsStyle(myPeakList) <- seqlevelsStyle(annoGR)
    ChIPpeakAnno:::bdp(myPeakList, annoGR)
  }

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.