preprocess MSstats file coming from FragPipe

Usage

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

Arguments

quant_data: path to MSstats csv 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
hierarchy_depth: hierarchy depth for aggregation