fga: Fraction Genome Altered

In CINmetrics: Calculate Chromosomal Instability Metrics

Description

Fraction Genome Altered looks at the fraction of the genome that deviates from a diploid state fga calculates the fraction of the genome altered (FGA; [Chin SF, et. al.](https://www.ncbi.nlm.nih.gov/pubmed/17925008)), measured by taking the sum of the number of bases altered and dividing it by the genome length covered ($G$). Genome length covered was calculated by summing the lengths of each probe on the Affeymetrix 6.0 array. This calculation **excludes** sex chromosomes.

Fraction\ Genome\ Altered = \frac {∑^{R}_{i = 1} d_i} {G} \ \ where\ |\bar{y}_{S_i}| ≥ 0.2

Usage

fga(cnvData, segmentMean = 0.2, numProbes = NA, genomeSize = 2873203431)

Arguments

cnvData	dataframe containing following columns: Sample, Start, End, Num_Probes, Segment_Mean
segmentMean	numerical value for the minimum segment_mean cutoff/ threshold. Default is 0.2
numProbes	Number of Probes
genomeSize	Size of the genome derived from Affymetrix 6.0 array probe. Default is 2873203431 calculated based on hg38 **excluding sex chromosomes**

Value

Fraction of the genome altered

Examples

fga(cnvData = maskCNV_BRCA)

CINmetrics documentation built on Aug. 2, 2021, 9:06 a.m.