Accessor functions for DEXSeqDataSet details

Description

Accessor functions of the DEXSeqDataSet object.

Usage

  featureCounts(object, normalized=FALSE)

  featureIDs( object )
  featureIDs( object ) <- value

  exonIDs( object )
  exonIDs( object ) <- value

  groupIDs( object )
  groupIDs( object ) <- value

  geneIDs( object )
  geneIDs( object ) <- value

  sampleAnnotation( object )
  

Arguments

Value

'featureCounts' access the counts per exonic region or feature region names. 'featureIDs' and 'exonIDs' are accessor functions for the exon bin or features identifiers. 'groupIDs' and 'geneIDs' are accessor functions for the character vector grouping the features, for example exonIDs from the same gene are grouped together by having the same value in the geneIDs. 'sampleAnnotation' is an accessor for the information from the samples.

Examples

  data(pasillaDEXSeqDataSet, package="pasilla")
  head( featureCounts( dxd ) )
  head( featureIDs(dxd))
  head( exonIDs(dxd))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(DEXSeq)
Loading required package: BiocParallel
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: DESeq2
Loading required package: AnnotationDbi
Loading required package: RColorBrewer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DEXSeq/accessors.Rd_%03d_medium.png", width=480, height=480)
> ### Name: featureCounts
> ### Title: Accessor functions for DEXSeqDataSet details
> ### Aliases: featureCounts featureIDs featureIDs<- exonIDs exonIDs<-
> ###   groupIDs groupIDs<- geneIDs geneIDs<- sampleAnnotation
> 
> ### ** Examples
> 
>   data(pasillaDEXSeqDataSet, package="pasilla")
>   head( featureCounts( dxd ) )
                 treated1fb treated2fb treated3fb untreated1fb untreated2fb
FBgn0000256:E001         92         28         43           54          131
FBgn0000256:E002        124         80         91           76          224
FBgn0000256:E003        340        241        262          347          670
FBgn0000256:E004        250        189        201          219          507
FBgn0000256:E005         96         38         39           71           76
FBgn0000256:E006          1          0          1            0            2
                 untreated3fb untreated4fb
FBgn0000256:E001           51           49
FBgn0000256:E002           82           95
FBgn0000256:E003          260          297
FBgn0000256:E004          242          250
FBgn0000256:E005           57           62
FBgn0000256:E006            0            2
>   head( featureIDs(dxd))
[1] "E001" "E002" "E003" "E004" "E005" "E006"
>   head( exonIDs(dxd))
[1] "E001" "E002" "E003" "E004" "E005" "E006"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>