annoByGenesAndCyto {BubbleTree} | R Documentation

## annoByGenesAndCyto

### 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, 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)

[Package BubbleTree version 2.12.0 Index]