bafTrack {BubbleTree} | R Documentation |
get the BAF track
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)
.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 |
the highlighted BAF track
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]])