annotateWithGeneParts-methods: Annotate given object with promoter, exon, intron and...

In genomation: Summary, annotation and visualization of genomic data

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

genomation documentation built on Nov. 8, 2020, 5:21 p.m.