annoPeaks: Annotate peaks

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

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,
  select = c("all", "bestOne"),
  ...
)

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, which means upstream. And the sec ond one must be no less than 1, which means downstream (1 is the site position, 2 is the next base of the site position). For details, see bindingType.
ignore.peak.strand	ignore the peaks strand or not.
select	"all" or "bestOne". Return the annotation containing all or the best one. The "bestOne" is selected by the shortest distance to the sites and then similarity between peak and annotations. Ignored if bindingType is nearestBiDirectionalPromoters.
...	Not used.

Value

Output is a GRanges object of the annotated peaks.

Author(s)

Jianhong Ou

See Also

See Also as annotatePeakInBatch

Examples

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

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