fga: Fraction Genome Altered

In lasseignelab/CINmetrics: An R package for analyzing copy number aberrations as a measure of chromosomal instability

Fraction Genome Altered

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 {\sum^{R}_{i = 1} d_i} {G} \ \ where\ |\bar{y}_{S_i}| \ge 0.2

Usage

fga(
  cnvData,
  sample_column = 1,
  segmentMean = 0.2,
  numProbes = NA,
  genomeSize = 2873203431
)

Arguments

cnvData	dataframe containing following columns: Sample, Chromosome, Start, End, Num_Probes, Segment_Mean
sample_column	numerical value for the sample column number, default is 1
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)

lasseignelab/CINmetrics documentation built on March 23, 2023, 10:38 p.m.