preprocess_dummy

Description

preprocess_dummy

Usage

preprocess_dummy(
  quant_data,
  fasta_file,
  annotation,
  pattern_contaminants = "^zz|^CON|Cont_",
  pattern_decoys = "^REV_|^rev",
  nr_peptides = 1
)

Arguments

quant_data	path to quantification data file
fasta_file	path to fasta file(s)
annotation	annotation list from read_annotation
pattern_contaminants	regex pattern for contaminants
pattern_decoys	regex pattern for decoys
nr_peptides	accepted for interface uniformity but ignored (interface stub)

Value

A placeholder list matching the reader contract, with lfqdata and protein_annotation entries.