fga | R Documentation |

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
```

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

`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** |

Fraction of the genome altered

```
fga(cnvData = maskCNV_BRCA)
```

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