preprocess MSstats fragpipe

Description

preprocess MSstats fragpipe

Usage

preprocess_MSstats_FPDIA(
  quant_data,
  fasta_file,
  annotation,
  pattern_contaminants = "",
  pattern_decoys = "",
  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.