btpredict {BubbleTree} | R Documentation |
btpredict
btpredict(.Object) ## S4 method for signature 'BTreePredictor' btpredict(.Object)
.Object |
the object |
.Object populated with the predictions
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")