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 = ""
)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)