SomatiCA (version 2.2.0)

copynumberCorrected: Somatic copy number corrected by admixture rate.

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".

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)