PDtoMSstatsFormat: Import Proteome Discoverer files

In Vitek-Lab/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Import Proteome Discoverer files

Description

Import Proteome Discoverer files

Usage

PDtoMSstatsFormat(
  input,
  annotation,
  useNumProteinsColumn = FALSE,
  useUniquePeptide = TRUE,
  summaryforMultipleRows = max,
  removeFewMeasurements = TRUE,
  removeOxidationMpeptides = FALSE,
  removeProtein_with1Peptide = FALSE,
  which.quantification = "Precursor.Area",
  which.proteinid = "Protein.Group.Accessions",
  which.sequence = "Sequence",
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

input	PD report or a path to it.
annotation	name of 'annotation.txt' or 'annotation.csv' data which includes Condition, BioReplicate, Run information. 'Run' will be matched with 'Spectrum.File'.
useNumProteinsColumn	TRUE removes peptides which have more than 1 in # Proteins column of PD output.
useUniquePeptide	TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
removeFewMeasurements	TRUE (default) will remove the features that have 1 or 2 measurements across runs.
removeOxidationMpeptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
removeProtein_with1Peptide	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
which.quantification	Use 'Precursor.Area'(default) column for quantified intensities. 'Intensity' or 'Area' can be used instead.
which.proteinid	Use 'Protein.Accessions'(default) column for protein name. 'Master.Protein.Accessions' can be used instead.
which.sequence	Use 'Sequence'(default) column for peptide sequence. 'Annotated.Sequence' can be used instead.
use_log_file	logical. If TRUE, information about data processing will be saved to a file.
append	logical. If TRUE, information about data processing will be added to an existing log file.
verbose	logical. If TRUE, information about data processing wil be printed to the console.
log_file_path	character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If 'append = TRUE', has to be a valid path to a file.
...	additional parameters to 'data.table::fread'.

Value

data.frame in the MSstats required format.

Author(s)

Meena Choi, Olga Vitek

Examples

pd_raw = system.file("tinytest/raw_data/PD/pd_input.csv", 
                     package = "MSstatsConvert")
annot = system.file("tinytest/annotations/annot_pd.csv", package = "MSstats")
pd_raw = data.table::fread(pd_raw)
annot = data.table::fread(annot)

pd_imported = PDtoMSstatsFormat(pd_raw, annot, use_log_file = FALSE)
head(pd_imported)

Vitek-Lab/MSstats documentation built on Nov. 4, 2024, 3:08 p.m.