ternary.cnr: build ternary matrix from integer copy number data

Description Usage Arguments Details Examples

View source: R/ternary.cnr.R

Description

This function builds a ternary matrix from the cnr$X or cnr$genes. It was designed as a helper function to generate the input for infSCITE.

Usage

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ternary.cnr(X, gain = 3, amp = 20)

Arguments

X

a X matrix either the bins or genes

gain

an integer copy number value specifying the minimum number of copies to call a gain as 1

amp

an integer value to specify the minimum number of copies to call as a high level amplification e.g. double minute

Details

Because infSCITE was developed for mutation data, this function attempts to recreate the scenario where 0 is no alteration, 1 is a low level / impact alteration, and 2 is high level / impact alteration.

By default, a deletion i.e. copy number of 0 will be treated as a high level deletion, and a loss i.e. one copy as a 1. The diploid state is treated as 0 = No mutation

Examples

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data(cnr)

G <- ternary.cnr(cnr$genes[, c("CDK4", "MDM2")])

head(G)

SingerLab/gac documentation built on Aug. 14, 2021, 10:57 a.m.