recode_cna: Function to recode numeric CNA alteration values to factor...

In MSKCC-Epi-Bio/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data

Function to recode numeric CNA alteration values to factor values

Description

Function to recode numeric CNA alteration values to factor values

Usage

recode_cna(alteration_vector)

Arguments

alteration_vector

a vector of CNA alterations coded with any of the following levels: neutral, deletion, amplification, gain, loss, homozygous deletion, hemizygous deletion, loh, gain, high level amplification, 0, -1, -1.5, -2, 1, 2.

Details

CNA is coded to the following key based on key: values below

• "neutral": "0", "neutral",

• "deletion": "homozygous deletion", "-2",

• "deletion": "loh", "-1.5",

• "deletion": "hemizygous deletion", "-1",

• "amplification": "gain", "1",

• "amplification": high level amplification", "2",

Value

a recoded CNA data set with factor alteration values. See details for code dictionary

Examples

recode_cna(gnomeR::cna$alteration[1:10])

MSKCC-Epi-Bio/gnomeR documentation built on Oct. 17, 2024, 3:39 p.m.