genomation (version 1.4.2)

annotateWithGeneParts: 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)
## S3 method for class 'GRanges,GRangesList':
annotateWithGeneParts(target, feature,
  strand = FALSE, intersect.chr = FALSE)
## S3 method for class '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