expands (version 2.1.3)

simulation: Simulated heterogeneous samples

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

data(simulation)

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

# NOT RUN {
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')
# }