bafTrack: bafTrack

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

Description

get the BAF track

Usage

bafTrack(.Object, result.dat, gr2, somatic.gr = NULL, min.prev = 0.15,
  cex = 1.2)

## S4 method for signature 'TrackPlotter'
bafTrack(.Object, result.dat, gr2, somatic.gr = NULL,
  min.prev = 0.15, cex = 1.2)

Arguments

.Object	the object
result.dat	the result dataframe
gr2	the gr2 object
somatic.gr	somatic gr object annotation
min.prev	previous min
cex	the cex

Value

the highlighted BAF track

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "centromere.dat.rda", package="BubbleTree"))
load(system.file("data", "all.somatic.lst.RData", package="BubbleTree"))
load(system.file("data", "hg19.seqinfo.rda", package="BubbleTree"))

trackplotter <- new("TrackPlotter")
gr2 = centromere.dat
nn <- "sam2"
p2 <- bafTrack(trackplotter,
               result.dat=allCall.lst[[nn]]@result,
               gr2=gr2,
               somatic.gr=all.somatic.lst[[nn]])

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