annoByGenesAndCyto: annoByGenesAndCyto

In BubbleTree: BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

Description

get annotation for genes and cytobands

Usage

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)

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)

BubbleTree documentation built on Nov. 8, 2020, 8:22 p.m.