annoByGenesAndCyto {BubbleTree} | R Documentation |
get annotation for genes and cytobands
annoByGenesAndCyto(.Object, chr, beg, end, critical.genes, gene.uni.clean.gr, cyto.gr) ## S4 method for signature 'Annotate' annoByGenesAndCyto(.Object, chr, beg, end, critical.genes, gene.uni.clean.gr, cyto.gr)
.Object |
the objet |
chr |
the chromosome |
beg |
genomic start coord |
end |
genomic end coord |
critical.genes |
set of critical genes |
gene.uni.clean.gr |
gr object of genes |
cyto.gr |
gr object of cyto positions |
list of annotation for genes and cytobands
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)