annotate.WithFeature.Flank-methods: Annotate an object with two sets of genomic features

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

Description

The function annotates given genomic feature or methylKit object with two sets of annotation. It is primarily useful when annotating objects with CpG islands and shores.

Usage

  annotate.WithFeature.Flank(target,feature,flank,feature.name="feat",flank.name="flank",strand=FALSE)

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)
flank	a GRanges object storing chromosome locations of the flanks of the feature
feature.name	string for the name of the feature
flank.name	string for the name o
strand	If set to TRUE, annotation features and target features will be overlapped based on strand (def:FALSE)

Value

returns an annotationByFeature object

See Also

getMembers, getTargetAnnotationStats, getFeatsWithTargetsStats, plotTargetAnnotation

Examples

data(methylKit)
cpg.obj=read.feature.flank(system.file("extdata", "cpgi.hg18.bed.txt", package = "methylKit"),feature.flank.name=c("CpGi","shores"))

annotate.WithFeature.Flank(methylDiff.obj,cpg.obj$CpGi,cpg.obj$shores,feature.name="CpGi",flank.name="Shores")

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