extractRanges: Create a GRanges object from 'dmrcate' output.

In DMRcate: Methylation array and sequencing spatial analysis methods

Description

Takes a DMResults object and produces the corresponding GRanges object.

Usage

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

Arguments

dmrcoutput	A DMResults object.
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

library(ExperimentHub)
library(limma)
eh <- ExperimentHub()
FlowSorted.Blood.EPIC <- eh[["EH1136"]]
tcell <- FlowSorted.Blood.EPIC[,colData(FlowSorted.Blood.EPIC)$CD4T==100 |
                                colData(FlowSorted.Blood.EPIC)$CD8T==100]
detP <- detectionP(tcell)
remove <- apply(detP, 1, function (x) any(x > 0.01))
tcell <- tcell[!remove,]
tcell <- preprocessFunnorm(tcell)
#Subset to chr2 only
tcell <- tcell[seqnames(tcell) == "chr2",]
tcellms <- getM(tcell)
tcellms.noSNPs <- rmSNPandCH(tcellms, dist=2, mafcut=0.05)
tcell$Replicate[tcell$Replicate==""] <- tcell$Sample_Name[tcell$Replicate==""]
tcellms.noSNPs <- avearrays(tcellms.noSNPs, tcell$Replicate)
tcell <- tcell[,!duplicated(tcell$Replicate)]
tcell <- tcell[rownames(tcellms.noSNPs),]
colnames(tcellms.noSNPs) <- colnames(tcell)
assays(tcell)[["M"]] <- tcellms.noSNPs
assays(tcell)[["Beta"]] <- ilogit2(tcellms.noSNPs)
type <- factor(tcell$CellType)
design <- model.matrix(~type) 
myannotation <- cpg.annotate("array", tcell, arraytype = "EPIC",
                             analysis.type="differential", design=design, coef=2)
dmrcoutput <- dmrcate(myannotation, lambda=1000, C=2)
results.ranges <- extractRanges(dmrcoutput, genome = "hg19")

DMRcate documentation built on Jan. 17, 2021, 2 a.m.