simulation: Simulated heterogeneous samples

Description Usage Format Examples

Description

A total of 50 samples with various numbers of subpopulations per sample were simulated at variable noise rates and constant number of 200 mutations per sample.

Usage

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Format

List with 50 entries - one per simulated sample. Subpopulation composition can be predicted for each sample and the predictions compared to the the simulated entries:
snv - the matrix of simulated point mutations (including ground truth columns SP*, PM*).
cbs - the matrix of simulated copy number segments (including ground truth columns SP*).
spstats - matrix of subpopulation statistics (ground truth).

Examples

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data(simulation)
snvcols=c("chr", "startpos", "CN_Estimate", "AF_Tumor","PN_B")
cbscols=c("chr", "startpos", "endpos")
sI=1:50;#set to 1:200 to run on entire simulation
#out=runExPANdS(simulation[[1]]$snv[sI,snvcols],simulation[[1]]$cbs[,cbscols],plotF = 0);
#truePhy=buildPhylo(simulation[[1]]$cbs,outF='truePhylo'); ##simulated 
#predPhy=buildPhylo(out$sp_cbs,outF='truePhylo'); ##predicted
#par(mfrow=c(1,2))
#plot(truePhy$tree,cex=2,main='simulated')
#plot(predPhy$tree,cex=2,main='predicted')

noemiandor/expands documentation built on July 2, 2018, 4:17 a.m.