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Preprocess simulated data

Source: R/preprocess_SIM.R
preprocess_SIM.Rd

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
)

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

Value

list with lfqdata (LFQData) and protein_annotation (ProteinAnnotation)

Details

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