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.
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).
1 2 3 4 5 6 7 8 9 10
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[]$snv[sI,snvcols],simulation[]$cbs[,cbscols],plotF = 0); #truePhy=buildPhylo(simulation[]$cbs,outF='truePhylo'); ##simulated #predPhy=buildPhylo(out$sp_cbs,outF='truePhylo'); ##predicted #par(mfrow=c(1,2)) #plot(truePhy$tree,cex=2,main='simulated') #plot(predPhy$tree,cex=2,main='predicted')
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.