GS Reference Mapper data import

Description

This is an example of an link{MapperSet-class} object containing the output of Roche's GS Reference Mapper Software. It consists of 3 samples and 111 variants.

Usage

data(mapperSetExample)

Format

Formal class 'MapperSet'

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(mapperSetExample)
    mapperSetExample

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/mapperSetExample.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mapperSetExample
> ### Title: GS Reference Mapper data import
> ### Aliases: mapperSetExample
> ### Keywords: datasets
> 
> ### ** Examples
> 
>     data(mapperSetExample)
>     mapperSetExample
MapperSet (storageMode: list)
assayData: 111 features, 3 samples 
  element names: variantForwCount, totalForwCount, variantRevCount, totalRevCount 
protocolData: none
phenoData
  sampleNames: N01 N03 N04
  varLabels: accessionNumber
  varMetadata: labelDescription
featureData
  featureNames: 1 2 ... 111 (111 total)
  fvarLabels: chr strand ... knownSNP (8 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>