integIRTy (version 1.0.8)

dichotomizeMethy: 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)

Value

A binary matrix of the same dimension of input methy.

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.

Author

Pan Tong ([e-mail]), Kevin R Coombes ([e-mail])

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]