degDefault: Method to get the default table to use.

In DEGreport: Report of DEG analysis

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")

DEGreport documentation built on Nov. 8, 2020, 7:23 p.m.