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"

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 1.16.0 Index]