BubbleTree (version 2.2.2)

annoByGenesAndCyto: annoByGenesAndCyto

Description

get annotation for genes and cytobands

Usage

annoByGenesAndCyto(.Object, chr, beg, end, critical.genes, gene.uni.clean.gr, cyto.gr)
"annoByGenesAndCyto"(.Object, chr, beg, end, critical.genes, gene.uni.clean.gr, cyto.gr)

Arguments

.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

Value

list of annotation for genes and cytobands

Examples

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, [e-mail]) + 
    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)