Differential expression analysis (DESeq2 wrapper)

Performs a DESeq2-based differential expression workflow on the provided expression data. Automatically constructs the design formula if needed, runs DESeq, extracts results for one or more contrasts, optionally applies LFC shrinkage, and returns sorted tables.

Usage

diffExpAnalysis(exp_data, design, lfcShrink = TRUE, contrasts = NULL)

Arguments

exp_data

A count matrix, SummarizedExperiment containing raw counts and colData for samples.

design

A string or formula (without “~”) specifying the model design (e.g. `"condition"` or `~ condition + batch`). If no leading `~` is found, it is added automatically.

lfcShrink

Logical; if TRUE (default), performs log₂ fold‑change shrinkage on each result table via DESeq2::lfcShrink.

contrasts

Character vector of named results to extract (as returned by DESeq2::resultsNames). If NULL (default), all names except the intercept are used.

Value

A named list of data.frames (one per contrast), each sorted by adjusted p‑value then log₂ fold change. If only one contrast is specified, returns a single (unnamed) data.frame.

Details

- Internally builds or coerces a DESeqDataSet from `exp_data` and `design`. - Runs DESeq2::DESeq on the dataset. - For each contrast, retrieves results with DESeq2::results and optionally applies shrinkage.