Accessor function for the dispTable information in a CountDataSet

Description

The dispersion table ("dispTable") is a named vector that assigns to each condition (as name) a dispersion column (as value). If nbinomTest is called to compare two conditions, say "A" and "B", DESeq looks up in the dispTable, which dispersion columns to use. In the standard case (see example), these are just the dispersions for "A" and "B", i.e., the columns disp_A and disp_B in fData(object). If the "pooled" or "blind" variance estimation is used, all conditions are assigned the same column.

Usage

dispTable(object,...)

Arguments

Author(s)

Simon Anders, sanders@fs.tum.de

See Also

estimateDispersions, nbinomTest

Examples

   cds <- makeExampleCountDataSet()
   cds <- estimateSizeFactors( cds )
   cds <- estimateDispersions( cds )
   dispTable( cds )

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(DESeq)
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: 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: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DESeq/dispTable.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dispTable
> ### Title: Accessor function for the dispTable information in a
> ###   CountDataSet
> ### Aliases: dispTable dispTable,CountDataSet-method
> 
> ### ** Examples
> 
>    cds <- makeExampleCountDataSet()
>    cds <- estimateSizeFactors( cds )
>    cds <- estimateDispersions( cds )
>    dispTable( cds )
       A        B 
"pooled" "pooled" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>