ChIPpeakAnno (version 3.6.5)

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)

startSite

start position of the feature (strand is considered)

endSite

end position of the feature (strand is considered)

fullRange

whole range of the feature

nearestBiDirectionalPromoters

nearest promoters from both direction of the peaks (strand is considered). It will report bidirectional promoters if there are promoters in both directions in the given region (defined by bindingRegion). Otherwise, it will report the closest promoter in one direction.

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

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