heteroLociTrack: heteroLociTrack

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

Description

get the heteroLoci track

Usage

heteroLociTrack(.Object, result.dat, gr2, hetero.gr = NULL, min.prev = 0.15,
  ymax = 4.3, cex = 0.5)

## S4 method for signature 'TrackPlotter'
heteroLociTrack(.Object, result.dat, gr2,
  hetero.gr = NULL, min.prev = 0.15, ymax = 4.3, cex = 0.5)

Arguments

.Object	the object
result.dat	the results
gr2	the gr2 object
hetero.gr	hetero annotation
min.prev	previous min
ymax	max y
cex	the cex

Value

the highlightted heterozygosity track

Examples

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


trackplotter <- new("TrackPlotter")
gr2 = centromere.dat
nn <- "sam2"
z1 <- heteroLociTrack(trackplotter, allCall.lst[[nn]]@result, 
                      gr2, allHetero.lst[[nn]])

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