preprocess_msstats – prolfquapp

preprocess MSstats file coming from FragPipe

Description

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,
  nr_peptides = 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

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

Value

A list containing the prepared LFQData and ProteinAnnotation objects.