R: Annotate given object with promoter, exon, intron and...

annotateWithGeneParts {genomation}

R Documentation

Annotate given object with promoter, exon, intron and intergenic regions

Description

The function annotates GRangesList or GRanges object as overlapping with promoter,exon,intron or intergenic regions.

Usage

annotateWithGeneParts(target, feature, strand = FALSE,
  intersect.chr = FALSE)

## S4 method for signature 'GRanges,GRangesList'
annotateWithGeneParts(target, feature,
  strand = FALSE, intersect.chr = FALSE)

## S4 method for signature 'GRangesList,GRangesList'
annotateWithGeneParts(target, feature,
  strand = FALSE, intersect.chr = FALSE)

Arguments

`target`	`GRanges` or `GRangesList` object storing chromosome locations to be annotated (e.g. chipseq peaks)
`feature`	GRangesList object containing GRanges object for promoter, exons, introns and transcription start sites, or simply output of readTranscriptFeatures function
`strand`	If set to TRUE, annotation features and target features will be overlapped based on strand (def:FALSE)
`intersect.chr`	boolean, whether to select only chromosomes that are common to feature and target. FALSE by default

Value

AnnotationByGeneParts object or a list of AnnotationByGeneParts objects if target is a GRangesList object.

Examples

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

[Package genomation version 1.19.1 Index]