Creating a MapperSet

Description

This function imports a project of Roche's GS Reference Mapper Software. It stores all information into an instance of the Biobase ExpressionSet.

Usage

MapperSet(dirs, samplenames)

Arguments

Details

An instance of the MapperSet is derived from the Biobase eSet and thus structured into

1. assayData

variantForwCount/variantRevCount:

Contain the number of reads with the respective difference in forward/reverse direction.

totalForwCount/totalRevCount:

Contain the total coverage for every variant in forward/reverse direction.

2. featureData

chromosome, start/end:

Give the location of each variant.

referenceBases/variantBase:

Show the bases changed in each variant.

regName:

The name of the region (gene) where the variant is located.

knownSNP:

Lists Ensembl variant-ids for known SNPs (if any).

3. phenoData

By default, the phenoData contains the accession number of every sample.

Value

An instance of the MapperSet.

Author(s)

Christoph Bartenhagen

See Also

AVASet-class

Examples

# load a GS Mapper dataset containing 3 samples and 111 variants
data(mapperSetExample)
mapperSetExample

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/MapperSet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MapperSet
> ### Title: Creating a MapperSet
> ### Aliases: MapperSet MapperSet,character-method
> 
> ### ** Examples
> 
> # load a GS Mapper dataset containing 3 samples and 111 variants
> 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 
>