Description Usage Arguments Value Author(s) Examples
Plots an individual DMR (in context of possibly other DMRs) as found by dmrcate
.
Heatmap and mean methylation plots are shown as well as genomic coordinates
and proximal coding regions.
1 2 3 4 |
ranges |
A GRanges object (ostensibly created by |
dmr |
Index of |
CpGs |
Either: - A matrix of beta values for plotting, with unique Illumina probe IDs as rownames. - A GenomicRatioSet, annotated with the appropriate array and data types - A GRanges object describing individual CpGs to be plotted, containing methylated reads and total coverage for each sample. Please see the worked example in the vignette for the correct structure of this object. |
what |
Does |
arraytype |
Is |
phen.col |
Vector of colors denoting phenotypes of all samples described in
|
genome |
Reference genome for annotating DMRs. Can be one of |
samps |
Vector of samples to be plotted, corresponding to indices of |
... |
Extra arguments passed to |
A plot to the current device.
Aaron Statham <a.statham@garvan.org.au>, Tim J. Peters <t.peters@garvan.org.au>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## 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")
groups <- c(Tumour="magenta", Normal="forestgreen")
cols <- groups[as.character(type)]
samps <- c(1:6, 38+(1:6))
DMR.plot(ranges=results.ranges, dmr=1, CpGs=myBetas, what="Beta", arraytype = "450K",
phen.col=cols, genome="hg19", samps=samps)
## End(Not run)
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