subsetProbes {skewr} | R Documentation |
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).
subsetProbes(object, allele = c("M", "U"), type = c("I-red", "I-green", "II"), cg = TRUE, snps = TRUE, idmr = TRUE, ch = FALSE)
object |
A |
allele |
Should methylated or unmethylated data for the probes be returned. |
type |
May be |
cg |
Logical; Should the returned dataset contain the CpG probes. The default is |
snps |
Logical; Should the returned dataset conain the rs probes. The default is |
idmr |
Logical; should the returned dataset include probes that interrogate imprinted gene sites as given by Pidsley et al.(2013). The default is |
ch |
Logical; should the returned dataset include the non-CpG (ch) probes. The default if |
A matrix
Ryan Putney ryanputney@gmail.com
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.
if(require('wateRmelon')) { data(melon) melon.meth.II <- subsetProbes(melon, 'M', 'II') }