genomeDoubling: CNomplexity::genomeDoubling

In SteeleCD/CNomplexity: Analysis of Complex Copy Cumber and Structural Variants in Cancer Genomes.

Description

Identify samples that are genome doubled.

Usage

genomeDoubling(segFile,armFile=NULL,nReps=1000,
                       scoreFUN=ABSOLUTEscore,doSim=TRUE,
                       withCNb=TRUE,sampleCol = 1,aCol = 9,
                       bCol = 10,startCol = 4,endCol = 5,
                       chromCol = 3,totCol = 11,head=TRUE,
                       diag=FALSE,sepP=FALSE,doParallel=FALSE,
                       nCores = NULL) 

Arguments

segFile	Segment file.
armFile	Cytoband file. If NULL, default will be loaded.
nReps=1000	Number of simulations.
scoreFUN=ABSOLUTEscore	Score to get p value.
doSim=TRUE	Whether to simulate.
withCNb=TRUE	Does seg file have b CN?.
sampleCol	Seg sample column.
aCol	Seg a CN column.
bCol	Seg b CN column.
startCol	Seg start column.
endCol	Seg end column.
chromCol	Seg chrom column.
totCol	Seg total CN column.
head=TRUE	Does seg file have headers?.
diag=FALSE	Whether to output diagnosis objects..
sepP=FALSE	Vars separate for each allele?.
doParallel=FALSE	Run in parallel?.
nCores	Number of cores.

Details

Implements tests for genome doubling from Dewhurst et al. (2013) and Carter et al. (2012).

Value

Vector of p-values for genome doubling in each sample.

SteeleCD/CNomplexity documentation built on May 29, 2019, 2:09 p.m.