generateProfile: panConusig::generateProfile

In UCL-Research-Department-of-Pathology/panConusig: Pan-cancer copy number signatures analysis

panConusig::generateProfile

Description

Simulate a copy number profile from any combination of the following processes: "focal gain","focal loss","chromothripsis","translocation","chromoplexy","BFB","aneuploidy gain","aneuploidy loss","chromoanasynthesis", as well as whole genome doubling.

Usage

generateProfile(nAltBeforeGD=20,
                           doGD=FALSE,
                           nAltAfterGD=20,
                           probs=NULL,
                           chroms=NULL,
                           index=NULL,
                           doCN=TRUE)

Arguments

nAltBeforeGD	Integer. Number of alterations to simulate before any genome doubling.
doGD	Boolean. Whether to simulate a genome doubling event.
nAltAfterGD	Integer. Number of alterations to simulate after any genome doubling.
probs	Probabilities to simulate any given process. If given, should be a length 9 vector representing the probabilities for: "focal gain","focal loss","chromothripsis","translocation","chromoplexy","BFB","aneuploidy gain","aneuploidy loss","chromoanasynthesis".
chroms	List. Set of chromosomes to begin the simulation with. If NULL an unaltered genome is used to start the simulation.
index	Integer vector. If given, this restricts alterations to the chromosomes in chroms that match the index.
doCN	Boolean. Should the output be converted from a list of derivative chromosomes to a segment file?

Value

if doCN==TRUE: A segment file with columns sample, chr, start, end. If doCN==FALSE: A list of derivative chromosomes.

UCL-Research-Department-of-Pathology/panConusig documentation built on March 25, 2022, 12:18 a.m.