loadRBD: loadRBD

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

Description

load the RBD data

Usage

loadRBD(.Object, rbd, total.mark = NA)

## S4 method for signature 'BTreePredictor'
loadRBD(.Object, rbd, total.mark = NA)

Arguments

.Object	the object
rbd	rbd object
total.mark	total mark

Value

.Object populated with the RBD list with updated segment size

Examples

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

nn <- "sam6"

rbd <- allRBD.lst[[nn]]
btreepredictor@config$high.ploidy <- high.ploidy[nn]
btreepredictor@config$high.purity <- high.purity[nn]
btreepredictor <- loadRBD(btreepredictor, rbd)

BubbleTree documentation built on Nov. 8, 2020, 8:22 p.m.