CINmetrics (version 0.1.0)

fga: 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, 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

# NOT RUN {
fga(cnvData = maskCNV_BRCA)
# }