| fga {CINmetrics} | R Documentation |
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
fga(cnvData = maskCNV_BRCA)