DEGSet: DEGSet

In lpantano/DEGreport: Report of DEG analysis

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)

as.DEGSet(object, ...)

## S4 method for signature 'TopTags'
as.DEGSet(object, default = "raw", extras = NULL)

## S4 method for signature 'data.frame'
as.DEGSet(object, contrast, default = "raw", extras = NULL)

## S4 method for signature 'DESeqResults'
as.DEGSet(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 when using as.DEGSet.
...	Optional parameters of the generic.
extras	List of extra tables related to the same comparison when using as.DEGSet.
contrast	To name the comparison when using as.DEGSet.

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)
library(edgeR)
library(limma)
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)
deg(res, tidy = "tibble")
# From edgeR
dge <- DGEList(counts=counts(dds), group=colData(dds)[["treatment"]])
dge <- estimateCommonDisp(dge)
res <- as.DEGSet(topTags(exactTest(dge)))
# From limma
v <- voom(counts(dds), model.matrix(~treatment, colData(dds)), plot=FALSE)
fit <- lmFit(v)
fit <- eBayes(fit, robust=TRUE)
res <- as.DEGSet(topTable(fit, n = "Inf"), "A_vs_B")

lpantano/DEGreport documentation built on Feb. 28, 2024, 12:01 a.m.