Putative breakpoints of chimeric reads

Description

This example holds two consensus (pathogenic and reciproce) breakpoints of 12 chimeric reads indicating an inversion on chromosome 16. The Breakpoints object gives access to the breakpoint locations as well as alignment information for each of the 12 reads.

Usage

data(breakpoints)

Format

Formal class 'Breakpoints'

Source

‘Targeted next-generation sequencing detects point mutations, insertions, deletions, and balanced chromosomal rearrangements as well as identifies novel leukemia-specific fusion genes in a single procedure’ (Leukemia, submitted)

Examples

    data(breakpoints)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(R453Plus1Toolbox)
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/R453Plus1Toolbox/breakpoints.Rd_%03d_medium.png", width=480, height=480)
> ### Name: breakpoints
> ### Title: Putative breakpoints of chimeric reads
> ### Aliases: breakpoints
> ### Keywords: datasets
> 
> ### ** Examples
> 
>     data(breakpoints)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>