bafTrack: bafTrack

Description Usage Arguments Value Examples

Description

get the BAF track

Usage

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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

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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.