getMembers-methods: Get the membership slot of annotationByFeature
In fortunatobianconi/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results
Description
Usage
Arguments
Value
Examples
Description
Membership slot defines the overlap of target features
with annotation features as a matrix.
Usage
1
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
1
2
3
4
5
6
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)
fortunatobianconi/methylkit documentation built on May 16, 2019, 1:51 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Examples
Description
Membership slot defines the overlap of target features with annotation features as a matrix.
Usage
1 | getMembers(x)
|
Arguments
x |
an |
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
1 2 3 4 5 6 | 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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.