Estimate the dispersions for a DEXSeqDataSet

Description

This function obtains dispersion estimates for negative binomial distributed data for the specific case for DEXSeq.

Usage

## S4 method for signature 'DEXSeqDataSet'
estimateDispersions( object, fitType=c("parametric","local","mean"), maxit=100, niter=10, quiet=FALSE, formula=design(object), BPPARAM=SerialParam())

Arguments

Details

See ?estimateDispersions,DESeqDataSet-method for details.

Value

A DEXSeqDataSet with the dispersion information filled in as metadata columns.

Examples

  data(pasillaDEXSeqDataSet, package="pasilla")
  dxd <- estimateSizeFactors( dxd )
  dxd <- estimateDispersions( 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/estimateDispersions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: estimateDispersions
> ### Title: Estimate the dispersions for a DEXSeqDataSet
> ### Aliases: estimateDispersions estimateDispersions,DEXSeqDataSet-method
> 
> ### ** Examples
> 
>   data(pasillaDEXSeqDataSet, package="pasilla")
>   dxd <- estimateSizeFactors( dxd )
>   dxd <- estimateDispersions( dxd )
using supplied model matrix
using supplied model matrix
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>