DMR.plot: Plotting DMRs

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

Plotting DMRs

Description

Plots an individual DMR (in context of possibly other DMRs) as found by dmrcate. Heatmaps are shown as well as proximal coding regions, smoothed methylation values (with an option for smoothed group means) and chromosome ideogram.

Usage

DMR.plot(ranges, 
         dmr, 
         CpGs, 
         what = c("Beta", "M"), 
         arraytype = c("EPICv2", "EPICv1", "450K"),
         phen.col,
         genome = c("hg19", "hg38", "mm10"),
         labels = names(ranges),
         flank = 5000,
         heatmap = TRUE, 
         extra.ranges = NULL, 
         extra.title = names(extra.ranges))

Arguments

ranges	A GRanges object (ostensibly created by extractRanges()) describing DMR coordinates.
dmr	Index of ranges (one integer only) indicating which DMR to be plotted.
CpGs	Either: - A CpGannotated object (preferred), - A matrix of beta values for plotting, with unique Illumina probe IDs as rownames, - A GenomicRatioSet, annotated with the appropriate array and data types, or - A BSseq object containing per-CpG methylation and coverage counts for the samples to be plotted
what	Does CpGs (if a matrix) contain Beta or M-values? Not needed if object is a GenomicRatioSet or BSseq object.
arraytype	Is CpGs (if a matrix) sourced from EPIC or 450K data? Not needed if object is a GenomicRatioSet or BSseq object.
phen.col	Vector of colors denoting phenotypes of all samples described in CpGs. See vignette for worked example.
genome	Reference genome for annotating DMRs. Can be one of "hg19", "hg38" or "mm10"
labels	Vector of DMR names to be displayed. Defaults to names(ranges).
flank	Size, in base pairs, of the plotted region either side of the DMR. Cannot be less than 10bp or greater than 10kb.
heatmap	Should the heatmap be plotted? Default is TRUE, but FALSE is useful when plotting large numbers of samples.
extra.ranges	Optional GRanges object. Will plot any range overlapping a DMR..
extra.title	Vector of names for ranges from extra.ranges. Defaults to names(extra.ranges).

Value

A plot to the current device.

Author(s)

Tim J. Peters <[e-mail]>, Aaron Statham <[e-mail]>, Braydon Meyer <[e-mail]>

Examples

library(GenomicRanges)
library(AnnotationHub)
ah <- AnnotationHub()
EPICv2manifest <- ah[["AH116484"]]
dmrranges <- GRanges("chr2:86787856-86793994")
probes <- EPICv2manifest$IlmnID[EPICv2manifest$CHR=="chr2" & 
                                EPICv2manifest$MAPINFO > 86770000 &
                                EPICv2manifest$MAPINFO < 86810000]
probes <- probes[order(EPICv2manifest[probes, "MAPINFO"])]
object <- minfi::logit2(matrix(rbeta(length(probes)*10, 3, 1), 
                               length(probes), 10))
rownames(object) <- probes
object[9:35, 6:10] <- minfi::logit2(matrix(rbeta(135, 1, 3), 27, 5))
cols <- c(rep("forestgreen", 5), rep("magenta", 5))
names(cols) <- rep(c("Ctrl", "Treat"), each=5)
DMR.plot(dmrranges, dmr = 1, CpGs=object, what = "M", arraytype="EPICv2", 
         phen.col=cols, genome="hg38")

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