makeBedgraphs: Outputs bedGraphs

In timpeters82/DMRcate-release: Illumina 450K methylation array spatial analysis methods

Description

Makes bedGraphs, 1 per sample, each containing all significant regions found via dmrcate. Bedgraphs are written are written to the working directory.

Usage

makeBedgraphs(dmrcoutput, betas,
    annotation=c(array="IlluminaHumanMethylation450k",
        annotation="ilmn12.hg19"),
    samps=NULL)

Arguments

dmrcoutput	An object of class dmrcate.output.
betas	Matrix of beta values to be converted to bedGraph rows, with unique Illumina probe IDs as rownames.
annotation	A vector describing the type of annotation from which to derive bedgraph output. Identical context to minfi, i.e. annotation <- annotation(minfiobject) where minfiobject is a [Genomic](Methyl|Ratio)Set). Default (ilmn12.hg) is recommended.
samps	Vector of samples to be converted to bedGraph files, corresponding to columns of betas. Default is all samples plotted.

Value

Writes zero or more bedGraph files to the working directory.

Author(s)

Tim J. 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(myMs.noSNPs, analysis.type="differential",
    design=design, coef=39)
dmrcoutput <- dmrcate(myannotation, lambda=1000)
makeBedgraphs(dmrcoutput=dmrcoutput, betas=myBetas, samps=c(1,39))

## End(Not run)

timpeters82/DMRcate-release documentation built on May 31, 2019, 2:29 p.m.