annotateWithFeatures-methods: Annotate given ranges with genomic features

Description Usage Arguments Value See Also Examples

Description

The function annotates a target GRangesList or GRanges object as overlapping or not with the elements of a named GRangesList. This is useful to annotate your regions of interest with genomic features with arbitrary categories such as repeat classes or families, or output from genome segmentation alogorithms such as chromHMM.

Usage

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annotateWithFeatures(target, features, strand.aware = FALSE,
  intersect.chr = FALSE)

## S4 method for signature 'GRanges,GRangesList'
annotateWithFeatures(target, features,
  strand.aware = FALSE, intersect.chr = FALSE)

## S4 method for signature 'GRangesList,GRangesList'
annotateWithFeatures(target, features,
  strand.aware = FALSE, intersect.chr = FALSE)

Arguments

target

GRanges or GRangesList object storing chromosome locations to be annotated (e.g. chipseq peaks)

features

a named GRangesList object containing GRanges objects different set of features. The function calculates percent overlaps with and without precendence at the same time. The order of objects in GRangesList defines their precedence. If a range in target overlaps with a more precedent range in an element of features, the other overlaps from other less precedent elments will be discarded. This is useful for getting piecharts where percentages should add up to 100.

strand.aware

if set to TRUE, annotation features and target features will be overlapped based on strand (def:FALSE)

intersect.chr

logical value, whether to select only chromosomes that are common to feature and target. FALSE by default

Value

returns an AnnotationByFeature object or if target is a GRangesList, a list of AnnotationByFeature objects.

See Also

see getMembers, heatTargetAnnotation, plotTargetAnnotation

Examples

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library(GenomicRanges)
data(cage)
data(cpgi)
cage$tpm=NULL
gl = GRangesList(cage=cage, cpgi=cpgi)

bed.file = system.file("extdata/chr21.refseq.hg19.bed", package = "genomation")
gene.parts = readTranscriptFeatures(bed.file)
annot = annotateWithFeatures(gl, gene.parts, intersect.chr=TRUE)

genomation documentation built on Nov. 1, 2018, 2:12 a.m.