BubbleTree (version 2.2.2)

bafTrack: bafTrack

Description

get the BAF track

Usage

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