Function to recode numeric CNA alteration values to factor values

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.

Value

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

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",

Examples

recode_cna(gnomeR::cna$alteration[1:10])
#>  [1] deletion      amplification deletion      amplification deletion     
#>  [6] deletion      deletion      deletion      deletion      amplification
#> Levels: deletion amplification