annotate.WithGenicParts-methods: Annotate given object with gene annotation

In fortunatobianconi/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

The function annotates given genomic feature or methylKit object with gene annotation such as promoter, exon, intron & intergenic. It also gets the distance to nearest TSS (transcription start site) for each genomic feature or methylation event.

Usage

  annotate.WithGenicParts(target,GRangesList.obj,strand=FALSE)

Arguments

target	a methylDiff or a GRanges object storing chromosome locations to be annotated
GRangesList.obj	A GRangesList object containing GRanges object for promoter,exons,introns and TSSes, or simply output of read.transcript.features function
strand	If set to TRUE, annotation features and target features will be overlapped based on strand (def:FALSE)

Value

annotationByGenicParts object

See Also

getMembers, getTargetAnnotationStats, getFeatsWithTargetsStats, getAssociationWithTSS, plotTargetAnnotation

Examples

data(methylKit)
gene.obj=read.transcript.features(system.file("extdata", "refseq.hg18.bed.txt", package = "methylKit"))
annotate.WithGenicParts(methylDiff.obj, gene.obj)

fortunatobianconi/methylkit documentation built on May 16, 2019, 1:51 p.m.