extractRanges: Create GRanges object from 'dmrcate' output.

In rcavalcante/DMRcate: Methylation array and sequencing spatial analysis methods

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. <[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("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)

rcavalcante/DMRcate documentation built on May 21, 2019, 10:13 a.m.