run_qc_preprocess – prolfquapp

Preprocess quantification data for QC reporting

Description

Resolves configuration (from YAML or defaults), reads the annotation, and runs software-specific preprocessing. Returns everything needed to construct a QC_generator.

Usage

run_qc_preprocess(
  indir,
  dataset,
  software,
  yaml_file = NULL,
  outdir = "qc_dir",
  project = "",
  order = "",
  workunit = "",
  flat_outdir = FALSE
)

Arguments

indir directory containing quantification output files

dataset path to annotation CSV/TSV/XLSX

software software key (e.g. "DIANN", "SIM"); looked up in prolfqua_preprocess_functions

yaml_file optional path to config YAML; if it exists, used instead of generating a default config

outdir output directory (used only when no yaml_file)

project project ID (used only when no yaml_file)

order order ID (used only when no yaml_file)

workunit workunit ID (used only when no yaml_file)

flat_outdir when TRUE, write QC outputs directly into outdir without a dated subdir (default FALSE)

Value

list with xd (preprocessed data), files (discovered file paths), and config (ProlfquAppConfig)