extractRanges {DMRcate}R Documentation

Create GRanges object from dmrcate output.

Description

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

Usage

extractRanges(dmrcoutput, genome = c("hg19", "hg38", "mm10"))

Arguments

dmrcoutput

An object of class dmrcate.output.

genome

Reference genome for annotating DMRs with promoter overlaps. Can be one of "hg19", "hg38" or "mm10". Ranges are assumed to map to the reference stated; there is no liftover.

Value

A GRanges object.

Author(s)

Tim Triche Jr. <tim.triche@usc.edu>, Tim Peters <t.peters@garvan.org.au>

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("array", myMs.noSNPs, what="M", arraytype = "450K",
                             analysis.type="differential", design=design, coef=39)
dmrcoutput <- dmrcate(myannotation, lambda=1000, C=2)
results.ranges <- extractRanges(dmrcoutput, genome = "hg19")

## End(Not run)
[Package DMRcate version 1.18.0 Index]