Run differential expression analysis pipeline

Reads annotation, preprocesses quantification data, then runs the full DEA pipeline: aggregation, transformation, model fitting, and contrast computation. Returns the DEAnalyse object and supporting data needed for report generation.

Usage

run_dea(indir, dataset, software, config)

Arguments

indir

directory containing quantification output files

dataset

path to annotation CSV/TSV/XLSX

software

software key as returned by get_procfuncs (e.g. "prolfquapp.DIANN")

config

a ProlfquAppConfig object (already merged with CLI overrides via sync_opt_config)

Value

list with deanalyse (DEAnalyse), xd (preprocessed data), annotation (parsed annotation including contrasts), and files (discovered file paths)