copynumberCorrected: Somatic copy number corrected by admixture rate.

In SomatiCA: SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing

Description

Somatic copy number corrected by admixture rate.

Usage

copynumberCorrected(segment, admix)

Arguments

segment	A GRanges class, segments with annotation of somatic ratio.
admix	Numeric. Admixture rate of normal cells.

Value

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".

Author(s)

Mengjie Chen

Examples

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)

SomatiCA documentation built on Oct. 5, 2016, 4:18 a.m.