run_make_yaml – prolfquapp

Generate a DEA configuration list

Description

Creates a ProlfquAppConfig object, converts it to a plain list, and reorders fields so that verbose/internal sections appear at the bottom of the YAML output.

Usage

run_make_yaml(
  project = "",
  order = "",
  workunit = "",
  norm = "vsn",
  model = "lm_impute",
  nr_peptides = 1,
  outdir = NULL
)

Arguments

project project ID

order order ID

workunit workunit ID

norm normalization method (e.g. "vsn", "none", "robscale")

model contrast facade method (see names(prolfqua::FACADE_REGISTRY)) or "saint"

nr_peptides minimum distinct peptides per protein (>= 1, default 1)

outdir optional output directory; if it exists, stored in the config so downstream scripts know where to write results

Value

named list suitable for yaml::write_yaml()

Examples

library("prolfquapp")

cfg <- run_make_yaml(project = "p100", workunit = "WU123")
cfg$project_spec$workunit_Id

[1] "WU123"