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 alteration incidence matrix from copy number data. Anything not equal to base.ploidy is 1.

Usage

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

Arguments

X	a copy number matrix to convert to an incidence matrix
bulk	logical, if TRUE data is bulk DNA is cbioportal calls, default is FALSE for integer copy number
base.ploidy	expected ploidy, e.g. 2N = 2, 4N = 4

Value

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

Examples

data(cnr)

Z <- binary.X(cnr$X, bulk = cnr$bulk)

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

SingerLab/gac documentation built on March 29, 2025, 4:38 p.m.