run_dea – prolfquapp

Run differential expression analysis pipeline

Description

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), files (discovered file paths), software (resolved software key), and requested_software (software key requested by the caller)

Examples

library("prolfquapp")

dataset <- system.file(
  "application/sim_test/dataset_sim.csv",
  package = "prolfquapp"
)
config <- make_DEA_config_R6(
  PATH = tempdir(),
  application = "SIM",
  model = "lm"
)
result <- run_dea(tempdir(), dataset, "prolfquapp.SIM", config)
names(result)

[1] "deanalyse"          "xd"                 "annotation"        
[4] "files"              "software"           "requested_software"