dichotomizeMethy: Dichotomize the methylation data given both tumor and normal...

In integIRTy: Integrating Multiple Modalities of High Throughput Assays Using Item Response Theory

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 ([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]

integIRTy documentation built on Sept. 9, 2022, 3:09 p.m.