extractRanges: Create GRanges object from 'dmrcate' output.

In timpeters82/DMRcate-release: Illumina 450K methylation array spatial analysis methods

Description

Takes a dmrcate.output object and produces the corresponding GRanges object.

Usage

extractRanges(dmrcoutput)

Arguments

dmrcoutput

An object of class dmrcate.output.

Value

A GRanges object.

Author(s)

Tim Triche Jr. <[e-mail]>, Tim Peters <[e-mail]>

Examples

## Not run: 
data(dmrcatedata)
myMs <- logit2(myBetas)
myMs.noSNPs <- rmSNPandCH(myMs, dist=2, mafcut=0.05)
patient <- factor(sub("-.*", "", colnames(myMs)))
type <- factor(sub(".*-", "", colnames(myMs)))
design <- model.matrix(~patient + type) 
myannotation <- cpg.annotate(myMs.noSNPs, analysis.type="differential",
    design=design, coef=39)
dmrcoutput <- dmrcate(myannotation, lambda=1000)
myRanges <- extractRanges(dmrcoutput)

## End(Not run)

timpeters82/DMRcate-release documentation built on May 31, 2019, 2:29 p.m.