Learn R
ChIPpeakAnno (version 3.6.4)

annoPeaks: Annotate peaks

Description

Annotate peaks by annoGR object in the given range.

Usage

annoPeaks (peaks, annoData, 
          bindingType=c("nearestBiDirectionalPromoters",
                        "startSite", "endSite", "fullRange"), 
          bindingRegion=c(-5000, 5000), 
          ignore.peak.strand=TRUE,
          ...)

Arguments

peaks
peak list, GRanges object
annoData
annotation data, GRanges object
bindingType
Specifying the criteria to associate peaks with annotation. Here is how to use it together with the parameter bindingRegion
  • To obtain peaks within 5kb upstream and up to 3kb downstream of TSS within the gene body, set bindingType = "startSite" and bindingRegion = c(-5000, 3000)
  • To obtain peaks up to 5kb upstream within the gene body and 3kb downstream of gene/Exon End, set bindingType = "endSite" and bindingRegion = c(-5000, 3000)
  • To obtain peaks from 5kb upstream to 3kb downstream of genes/Exons , set bindingType = "fullRange" and bindingRegion = c(-5000, 3000)
  • To obtain peaks with nearest bi-directional promoters within 5kb upstream and 3kb downstream of TSS, set bindingType = "nearestBiDirectionalPromoters" and bindingRegion = c(-5000, 3000)
[object Object],[object Object],[object Object],[object Object]
bindingRegion
Annotation range used together with bindingType, which is a vector with two integer values, default to c (-5000, 5000). The first one must be no bigger than 0. And the sec ond one must be no less than 1. For details, see bindingType.
ignore.peak.strand
ignore the peaks strand or not.
...
Not used.

Value

  • Output is a GRanges object of the annotated peaks.

See Also

See Also as annotatePeakInBatch

Examples

Run this code
library(EnsDb.Hsapiens.v75)
    data("myPeakList")
    annoGR <- toGRanges(EnsDb.Hsapiens.v75)
    seqlevelsStyle(myPeakList) <- seqlevelsStyle(annoGR)
    annoPeaks(myPeakList, annoGR)

Run the code above in your browser using DataLab