Description Usage Arguments Value Author(s) Examples

Somatic copy number corrected by admixture rate.

1 | ```
copynumberCorrected(segment, admix)
``` |

`segment` |
A GRanges class, segments with annotation of somatic ratio. |

`admix` |
Numeric. Admixture rate of normal cells. |

A GRanges class, segments with annotation of event.

`seqnames, ranges ` |
See GRanges(). |

`medLAF ` |
A numeric vector. Median lesser allele frequency of each segment in the tumor sample. |

`ratio` |
A numeric vector. Somatic ratio (read depth ratio of tumor/normal) of each segment. |

`somaCN` |
An integer vector. Somatic integer copy number based on somatic ratio. |

`event` |
A character vector. Somatic event characterization based on somatic ratio, taking values of "=", "Loss", "Gain", "LOH", "neutral LOH" or "double deletion". |

Mengjie Chen

1 2 3 4 5 6 7 8 9 10 | ```
data(segwithratio)
x <- GRanges(seqnames=segwithratio$chromosome,
ranges=IRanges(start=segwithratio$start,
end=segwithratio$end),
medLAF=segwithratio$medLAF,
medgLAF=segwithratio$medgermlineLAF,
ratio=segwithratio$ratio
)
admix <- 0.4
y <- copynumberCorrected(x, admix)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.