Accessors for the 'dispersionFunction' slot of a DESeqDataSet object.

Description

The dispersion function is calculated by estimateDispersions and used by varianceStabilizingTransformation. Parametric dispersion fits store the coefficients of the fit as attributes in this slot.

Usage

dispersionFunction(object, ...)

dispersionFunction(object, ...) <- value

## S4 method for signature 'DESeqDataSet'
dispersionFunction(object)

## S4 replacement method for signature 'DESeqDataSet,'function''
dispersionFunction(object,
  estimateVar = TRUE) <- value

Arguments

Details

Setting this will also overwrite mcols(object)$dispFit and the estimate the variance of dispersion residuals, see estimateVar below.

See Also

estimateDispersions

Examples

dds <- makeExampleDESeqDataSet(m=4)
dds <- estimateSizeFactors(dds)
dds <- estimateDispersions(dds)
dispersionFunction(dds)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
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


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: GenomeInfoDb
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DESeq2/dispersionFunction.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dispersionFunction
> ### Title: Accessors for the 'dispersionFunction' slot of a DESeqDataSet
> ###   object.
> ### Aliases: dispersionFunction dispersionFunction,DESeqDataSet-method
> ###   dispersionFunction<-
> ###   dispersionFunction<-,DESeqDataSet,function-method
> 
> ### ** Examples
> 
> 
> dds <- makeExampleDESeqDataSet(m=4)
> dds <- estimateSizeFactors(dds)
> dds <- estimateDispersions(dds)
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
> dispersionFunction(dds)
function (q) 
coefs[1] + coefs[2]/q
<environment: 0x9b9df50>
attr(,"coefficients")
asymptDisp  extraPois 
0.09557337 7.05418523 
attr(,"fitType")
[1] "parametric"
attr(,"varLogDispEsts")
[1] 0.9026065
attr(,"dispPriorVar")
[1] 0.25
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>