preprocess_sim – prolfquapp

Preprocess simulated data

Description

Returns a simulated LFQData + ProteinAnnotation, bypassing all file I/O. Designed for integration testing of CMD scripts via –software SIM.

Usage

preprocess_SIM(
  quant_data,
  fasta_file,
  annotation,
  pattern_contaminants = "^zz|^CON|Cont_",
  pattern_decoys = "^REV_|^rev_",
  hierarchy_depth = 1,
  nr_peptides = 1
)

Arguments

quant_data ignored (placeholder)

fasta_file ignored (placeholder)

annotation annotation list from read_annotation

pattern_contaminants regex for contaminant proteins

pattern_decoys regex for decoy proteins

hierarchy_depth 1 = protein level, 2 = peptide level

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

Details

The simulated data is reconfigured to use the annotation’s factor prefix so that contrasts derived from the annotation match the model terms.

Value

list with lfqdata (LFQData) and protein_annotation (ProteinAnnotation)