binary.X: build binary matrix from integer copy number data

In SingerLab/gac: Genetic Analysis of Cells

build binary matrix from integer copy number data

Description

This function builds a binary, incidence, matrix from the cnr$X. It was designed as a helper function to generate the input for infSCITE.

Usage

binary.X(X, base.ploidy = 2)

Arguments

X	a copy number matrix to convert to an incidence matrix
base.ploidy	expected cell ploidy, e.g. 2N = 2, 4N = 4

Details

Because infSCITE was developed for mutation data, this function creates a precense/absence matrix of the data

By default, anything not diploid is 1.

Value

Returns an incidence matrix for X, when X != base.ploidy

Examples

data(cnr)

Z <- binary.X(cnr$genes[, c("CDK4", "MDM2")])

SingerLab/gac documentation built on March 16, 2023, 2:52 p.m.