methylKit (version 0.99.2)

getMembers: Get the membership slot of annotationByFeature

Description

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

Usage

getMembers(x)
# S4 method for annotationByFeature
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: annotateWithFeature, annotateWithFeatureFlank, annotateWithGenicParts

Examples

# NOT RUN {
data(methylKit)
cpg.obj=readFeatureFlank(system.file("extdata", "cpgi.hg18.bed.txt", 
package = "methylKit"),feature.flank.name=c("CpGi","shores"))

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

# }