Extract a matrix of model coefficients/standard errors

Description

Note: results tables with log2 fold change, p-values, adjusted p-values, etc. for each gene are best generated using the results function. The coef function is designed for advanced users who wish to inspect all model coefficients at once.

Usage

## S3 method for class 'DESeqDataSet'
coef(object, SE = FALSE, ...)

Arguments

Details

Estimated model coefficients or estimated standard errors are provided in a matrix form, number of genes by number of parameters, on the log2 scale. The columns correspond to columns of the model matrix for final GLM fitting, i.e., attr(dds, "modelMatrix").

Author(s)

Michael Love

Examples

dds <- makeExampleDESeqDataSet(m=4)
dds <- DESeq(dds)
coef(dds)[1,]
coef(dds, SE=TRUE)[1,]

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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/coef.Rd_%03d_medium.png", width=480, height=480)
> ### Name: coef
> ### Title: Extract a matrix of model coefficients/standard errors
> ### Aliases: coef coef.DESeqDataSet
> 
> ### ** Examples
> 
> 
> dds <- makeExampleDESeqDataSet(m=4)
> dds <- DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> coef(dds)[1,]
 Intercept conditionA conditionB 
 2.5110930  0.2890211 -0.2890195 
> coef(dds, SE=TRUE)[1,]
 SE_Intercept SE_conditionA SE_conditionB 
    0.8454642     0.2530218     0.2530218 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>