## ----results='hide', message=FALSE, warning=FALSE----------------------------- library(mitoClone2) ## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", tidy.opts=list(width.cutoff=70), tidy=TRUE ) ## ----setup-------------------------------------------------------------------- load(system.file("data/M_P1.RData",package = "mitoClone2")) load(system.file("data/N_P1.RData",package = "mitoClone2")) P1 <- mutationCallsFromMatrix(as.matrix(M_P1), as.matrix(N_P1)) ## ----runTreebuilding, message=FALSE------------------------------------------- ## this next step takes approx 4.1 minutes to run tmpd <- tempdir() dir.create(paste0(tmpd,'/p1')) P1 <- varCluster(P1, tempfolder=paste0(tmpd,'/p1'),method='SCITE') ## ----clusterClonesP1, fig.width=8,fig.height=6-------------------------------- P1 <- clusterMetaclones(P1, min.lik = 1) ## ----plotClonesP1, fig.width=8,fig.height=6----------------------------------- plotClones(P1) ## ----getmut2clone, fig.width=8,fig.height=6----------------------------------- m2c <- mitoClone2:::getMut2Clone(P1) print(m2c) ##To e.g. treat the mt:2537G>A and mt:14462:G>A mutations as a subclone ##distinct from CEBPA, we can assign them a new clonal identity m2c[c("X2537GA","X14462GA")] <- as.integer(6) P1.new <- mitoClone2:::overwriteMetaclones(P1, m2c) plotClones(P1.new) ## ----label='Session information', eval=TRUE, echo=FALSE----------------------- sessionInfo()