methylKit (version 0.99.2)

annotateWithGenicParts: Annotate given object with gene annotation

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

annotateWithGenicParts(target,GRangesList.obj,strand=FALSE)
# S4 method for GRanges,GRangesList
annotateWithGenicParts(target, GRangesList.obj,
  strand = FALSE)
# S4 method for methylDiff,GRangesList
annotateWithGenicParts(target,
  GRangesList.obj, strand = FALSE)
# S4 method for methylDiffDB,GRangesList
annotateWithGenicParts(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 readTranscriptFeatures 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

# NOT RUN {
data(methylKit)
gene.obj=readTranscriptFeatures(system.file("extdata", 
"refseq.hg18.bed.txt", package = "methylKit"))
annotateWithGenicParts(methylDiff.obj, gene.obj)
# }