| dichotomizeMethy {integIRTy} | R Documentation |
Dichotomize the methylation data given both tumor and normal controls.
Description
This function implements the procedure for dichotomizing methylation data described in the paper.
Usage
dichotomizeMethy(methy, methyCtr, refUseMean = FALSE)
Arguments
methy |
The methylation matrix for tumor samples. Each element represents the beta value which is bounded between 0 and 1. Rows are genes and columns are samples. |
methyCtr |
Methylation matrix of normal controls. Genes should exactly the same as the tumor sample. The sample size are not necessarily the same as tumor sample. |
refUseMean |
Logical indicating whether to use mean of normal sample as reference. Default is set to FALSE which means to use median as it is more robust. |
Value
A binary matrix of the same dimension of input methy.
Author(s)
Pan Tong (nickytong@gmail.com), Kevin R Coombes (krc@silicovore.com)
References
Tong P, Coombes KR. integIRTy: a method to identify altered genes in cancer accounting for multiple mechanisms of regulation using item response theory. Bioinformatics, 2012 Nov 15; 28(22):2861–9.
See Also
dichotomizeCN, dichotomizeExpr, dichotomize
Examples
data(OV)
binDat <- dichotomizeMethy(Methy_T[1:200, ], Methy_N[1:200, ])
binDat[15:20, 1:2]