examples/btpredict-Ex.R

In BubbleTree: BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

load(system.file("data", "allRBD.lst.RData", package="BubbleTree"))

btreepredictor <- new("BTreePredictor")
btreepredictor@config$cutree.h <- 0.15
high.ploidy <- rep(TRUE, length(allRBD.lst))
high.purity <- rep(TRUE, length(allRBD.lst))

high.ploidy[c("sam6",
              "ovary.wgs",
              "ovary.wes",
              "TCGA-06-0145-01A-01W-0224-08",
              "TCGA-13-1500-01A-01D-0472-01",
              "TCGA-AO-A0JJ-01A-11W-A071-09")] <- FALSE

high.purity[c("sam6", "ovary.wgs", "ovary.wes")] <- FALSE

rbd <- allRBD.lst[["sam6"]]
btreepredictor@config$high.ploidy <- high.ploidy["sam6"]
btreepredictor@config$high.purity <- high.purity["sam6"]
btreepredictor <- loadRBD(btreepredictor, rbd)
btreepredictor@config$min.segSize <- ifelse(max(btreepredictor@rbd$seg.size, 
                                                na.rm=TRUE) < 0.4, 0.1, 0.4)
btreepredictor <- btpredict(btreepredictor)
cat(info(btreepredictor), "\n")