annotateWithGeneParts {genomation} | R Documentation |
The function annotates GRangesList
or GRanges
object as
overlapping with promoter,exon,intron or intergenic regions.
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)
target |
|
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 |
AnnotationByGeneParts
object or a list of
AnnotationByGeneParts
objects if target is a GRangesList
object.
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