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

In timpeters82/DMRcate-devel: Methylation array and sequencing spatial analysis methods

Create a GRanges object from dmrcate output.

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(AnnotationHub)
library(GenomicRanges)
ah <- AnnotationHub()
EPICv2manifest <- ah[["AH116484"]]
chr21probes <- rownames(EPICv2manifest)[EPICv2manifest$CHR=="chr21"]
coords <- EPICv2manifest[chr21probes, "MAPINFO"]
stats <- rt(length(chr21probes), 2)
pvals <- pt(-abs(stats), 100)
fdrs <- p.adjust(2*pvals, "BH")
annotated <- GRanges(rep("chr21", length(stats)), IRanges(coords, coords), stat = stats,
                     rawpval = pvals, diff = 0, ind.fdr = fdrs, is.sig = fdrs < 0.05)
names(annotated) <- chr21probes
myannotation <- new("CpGannotated", ranges=annotated)
dmrcoutput <- dmrcate(myannotation, lambda=1000, C=2)
extractRanges(dmrcoutput, genome = "hg38")

timpeters82/DMRcate-devel documentation built on Dec. 19, 2024, 11:14 a.m.