degDefault {DEGreport} | R Documentation

## Method to get the default table to use.

### Description

It can accept a list of new padj values matching the same dimmensions than the current vector. It can calculate the `lfdr` based on fdrtool::fdrtool function.

### Usage

    degDefault(object)

    degCorrect(object, fdr)

    ## S4 method for signature 'DEGSet'
    degDefault(object)

    ## S4 method for signature 'DEGSet'
    degCorrect(object, fdr)

### Arguments

`object` | DEGSet
`fdr` | It can be `fdr-stat`, `fdr-pvalue`, vector of new padj

### Author(s)

Lorena Pantano

Lorena Pantano

### Examples

    library(DESeq2)
    library(dplyr)
    dds <- makeExampleDESeqDataSet(betaSD=1)
    colData(dds)[["treatment"]] <- sample(colData(dds)[["condition"]], 12)
    design(dds) <-  ~ condition + treatment
    dds <- DESeq(dds)
    res <- degComps(dds, contrast = list("treatment_B_vs_A"))
    # library(fdrtools); degCorrect(res, fdr = "lfdr-stat")

[Package DEGreport version 1.28.0 Index]