extractRanges {DMRcate} | R Documentation |
dmrcate
output.
Takes a dmrcate.output
object and produces the corresponding GRanges object.
extractRanges(dmrcoutput, genome = c("hg19", "hg38", "mm10"))
dmrcoutput |
An object of class |
genome |
Reference genome for annotating DMRs with promoter overlaps.
Can be one of |
A GRanges object.
Tim Triche Jr. <tim.triche@usc.edu>, Tim Peters <t.peters@garvan.org.au>
## 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)