subsetProbes: Conveniently subset probes by type and retrieve the methylated or unmethylated intensities

Description

Thus function accepts a MethyLumiSet object generated by methylumi or a MethylSet object generated by minfi. It will subset the probes by type--"I-red", "I-green", or "II"--and return a matrix of the methylated, "M", or unmethylated, "U" signal intensities. It is also possible to include or filter out probes according to whether they are CpG sites(cg), SNPs(rs), imprinted(idmr) gene sites, or non-CpG loci(ch).

Usage

subsetProbes(object, allele = c("M", "U"),
              type = c("I-red", "I-green", "II"),
              cg = TRUE, snps = TRUE, idmr = TRUE, ch = FALSE)

Arguments

object

A MethyLumiSet or MethylSet object

allele

Should methylated or unmethylated data for the probes be returned.

type

May be "I-red", "I-green", or {"II"}.

Logical; Should the returned dataset contain the CpG probes. The default is TRUE

snps

Logical; Should the returned dataset conain the rs probes. The default is TRUE

idmr

Logical; should the returned dataset include probes that interrogate imprinted gene sites as given by Pidsley et al.(2013). The default is TRUE

Logical; should the returned dataset include the non-CpG (ch) probes. The default if FALSE

Value

A matrix

References

Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalwyk LC(2013). A data-driven approach to preprocessing Illumina 450k methylation array data. BMC Genomics, 14:293.

Examples

Run this code

if(require('wateRmelon')) {
  data(melon)
  melon.meth.II <- subsetProbes(melon, 'M', 'II')
}