DEGSet {DEGreport} | R Documentation

## DEGSet

### Description

S4 class to store data from differentially expression analysis. It should be compatible with different package and stores the information in a way the methods will work with all of them.

### Usage

    DEGSet(resList, default)

    DEGSet(resList, default)

    DEGSetFromEdgeR(object, ...)

    DEGSetFromDESeq2(object, ...)

    ## S4 method for signature 'TopTags'
    DEGSetFromEdgeR(object, default = "shrunken",
      extras = NULL)

    ## S4 method for signature 'DESeqResults'
    DEGSetFromDESeq2(object, default = "shrunken",
      extras = NULL)

### Arguments

`resList` | List with results as elements containing log2FoldChange, pvalues and padj as column. Rownames should be feature names. Elements should have names.
`default` | The name of the element to use by default.
`object` | Different objects to be transformed to DEGSet.
`...` | Optional parameters of the generic.
`extras` | List of extra tables related to the same comparison.

### Details

For now supporting only `DESeq2::results()` output. Use constructor `degComps()` to create the object.

The list will contain one element for each comparison done. Each element has the following structure:

- DEG table

- Optional table with shrunk Fold Change when it has been done.

To access the raw table use `deg(dgs, "raw")`, to access the shrunken table use `deg(dgs, "shrunken")` or just `deg(dgs)`.

### Author(s)

Lorena Pantano

### Examples

    library(DESeq2)
    dds <- makeExampleDESeqDataSet(betaSD = 1)
    colData(dds)[["treatment"]] <- sample(colData(dds)[["condition"]], 12)
    design(dds) <-  ~ condition + treatment
    dds <- DESeq(dds)
    res <- degComps(dds, combs = c("condition"))
    deg(res[[1]])
    deg(res[[1]], tidy = "tibble")

[Package DEGreport version 1.16.0 Index]