coef {DESeq2} | R Documentation

## 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

`object` | a DESeqDataSet returned by `DESeq`, `nbinomWaldTest`, or `nbinomLRT`.
`SE` | whether to give the standard errors instead of coefficients. defaults to FALSE so that the coefficients are given.
`...` | additional 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,]

[Package DESeq2 version 1.26.0 Index]