annotate.WithFeature-methods: Annotate object with a set of genomic features

In vd4mmind/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

The function annotates given genomic feature or methylKit object with a set of annotation. It is primarily useful when annotating objects with simple genomic features, such as enhancer locations.

Usage

  annotate.WithFeature(target,feature,strand=FALSE,extend=0,feature.name="feat1")

Arguments

target	a methylDiff or a GRanges object storing chromosome locations to be annotated
feature	a GRanges object storing chromosome locations of a feature (can be CpG islands, ChIP-seq peaks, etc)
strand	If set to TRUE, annotation features and target features will be overlapped based on strand (def:FALSE)
extend	specifiying a positive value will extend the feature on both sides as much as extend
feature.name	name of the annotation feature. For example: H3K4me1,CpGisland etc.

Value

returns an annotationByFeature object

See Also

getMembers, getTargetAnnotationStats, getFeatsWithTargetsStats, plotTargetAnnotation

Examples

data(methylKit)
cpg.gr=read.bed(system.file("extdata", "cpgi.hg18.bed.txt", package = "methylKit"),remove.unsual=TRUE)

annotate.WithFeature(methylDiff.obj,cpg.gr,strand=FALSE,extend=0,feature.name="CpGi")

vd4mmind/methylkit documentation built on May 3, 2019, 4:57 p.m.