Accessor function for the fitInfo objects in a CountDataSet

Description

After calling estimateDispersions, a CountDataSet object is populated with one or (in case of a “per-condition” estimation) several fitInfo objects, which can be accessed with this function.

Usage

fitInfo( cds, name=NULL )

Arguments

Author(s)

Simon Anders, sanders@fs.tum.de

See Also

estimateDispersions

Examples

   cds <- makeExampleCountDataSet()
   cds <- estimateSizeFactors( cds )
   cds <- estimateDispersions( cds )
   str( fitInfo( 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/fitInfo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fitInfo
> ### Title: Accessor function for the fitInfo objects in a CountDataSet
> ### Aliases: fitInfo
> 
> ### ** Examples
> 
>    cds <- makeExampleCountDataSet()
>    cds <- estimateSizeFactors( cds )
>    cds <- estimateDispersions( cds )
>    str( fitInfo( cds ) )
List of 5
 $ perGeneDispEsts: num [1:10000] 0.0394 0.2999 0.335 0.3192 0.0798 ...
 $ dispFunc       :function (q)  
  ..- attr(*, "coefficients")= Named num [1:2] 0.219 0.864
  .. ..- attr(*, "names")= chr [1:2] "asymptDisp" "extraPois"
  ..- attr(*, "fitType")= chr "parametric"
 $ fittedDispEsts : num [1:10000] 0.22 0.22 0.221 0.227 0.227 ...
 $ df             : int 3
 $ sharingMode    : chr "maximum"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>