DESeqAnalysis: DESeq2 differential expression analysis

In steinbaugh/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

DESeq2 differential expression analysis

Description

Class containing all elements generated during differential expression analysis with DESeq2. This class is essentially a list with validity checks to ensure DESeqTransform and DESeqResults correspond to the DESeqDataSet.

Usage

DESeqAnalysis(data, transform, results, lfcShrink = NULL)

Arguments

data	DESeqDataSet.
transform	DESeqTransform. DESeq2::varianceStabilizingTransformation() recommended by default.
results	list or single DESeqResults. One or more unshrunken DESeqResults. Assign the DESeq2::results() return here.
lfcShrink	list, single DESeqResults, or NULL. Optional. One or more shrunken DESeqResults. Assign the DESeq2::lfcShrink() return here.

Value

DESeqAnalysis.

Note

Updated 2021-03-15.

Examples

suppressPackageStartupMessages({
    library(S4Vectors)
    library(SummarizedExperiment)
})
data <- DESeq2::makeExampleDESeqDataSet()
rowRanges <- AcidGenomes::emptyRanges(names = rownames(data))
mcols(rowRanges)[["geneId"]] <- paste0("id", seq_len(length(rowRanges)))
mcols(rowRanges)[["geneName"]] <- paste0("name", seq_len(length(rowRanges)))
rowRanges(data) <- rowRanges
data <- DESeq2::DESeq(data)
class(data)

transform <- DESeq2::varianceStabilizingTransformation(data)
class(transform)

resultsNames(data)
name <- resultsNames(data)[[2L]]
results <- DESeq2::results(data, name = name)
class(results)

lfcShrink <- DESeq2::lfcShrink(dds = data, res = results, coef = 2L)

results <- list(results)
names(results) <- name

lfcShrink <- list(lfcShrink)
names(lfcShrink) <- name

object <- DESeqAnalysis(
    data = data,
    transform = transform,
    results = results,
    lfcShrink = lfcShrink
)
print(object)

steinbaugh/DESeqAnalysis documentation built on Oct. 13, 2023, 5:39 a.m.