Nothing
load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "cancer.genes.minus2.rda", package="BubbleTree"))
load(system.file("data", "vol.genes.rda", package="BubbleTree"))
load(system.file("data", "gene.uni.clean.gr.rda", package="BubbleTree"))
load(system.file("data", "cyto.gr.rda", package="BubbleTree"))
comm <- btcompare(vol.genes, cancer.genes.minus2)
btreeplotter <- new("BTreePlotter", branch.col="gray50")
annotator <-new("Annotate")
nn <- "sam2"
cc <- allCall.lst[[nn]]
z <- drawBTree(btreeplotter, cc@rbd.adj) +
ggplot2::labs(title=sprintf("%s (%s)", nn, info(cc)))
out <- cc@result$dist %>%
filter(seg.size >= 0.1 ) %>%
arrange(gtools::mixedorder(as.character(seqnames)), start)
ann <- annoByGenesAndCyto(annotator,
as.character(out$seqnames),
as.numeric(out$start),
as.numeric(out$end),
comm$comm,
gene.uni.clean.gr=gene.uni.clean.gr,
cyto.gr=cyto.gr)
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