getMembers-methods: Get the membership slot of annotationByFeature

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

Description

Membership slot defines the overlap of target features with annotation features as a matrix.

Usage

  getMembers(x)

Arguments

x	an annotationByFeature object

Value

a matrix showing overlap of target features with annotation features. 1 for overlap, 0 for non-overlap. Each row in the matrix corresponds to a genomic feature that is annoted by one of the following functions: annotate.WithFeature, annotate.WithFeature.Flank, annotate.WithGenicParts

Examples

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

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

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