MetamorpheusToMSstatsPTMFormat: Import Metamorpheus files into PTM format

In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications

Import Metamorpheus files into PTM format

Description

Import Metamorpheus files into PTM format

Usage

MetamorpheusToMSstatsPTMFormat(
  input,
  annotation,
  fasta_path,
  input_protein = NULL,
  annotation_protein = NULL,
  use_unmod_peptides = FALSE,
  mod_ids = c("\\[Common Biological:Phosphorylation on S\\]"),
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeProtein_with1Feature = FALSE,
  summaryforMultipleRows = max,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL
)

Arguments

input	name of Metamorpheus output file, which is tabular format. Use the AllQuantifiedPeaks.tsv file from the Metamorpheus output.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate.
fasta_path	string containing path to the corresponding fasta file for the modified peptide dataset.
input_protein	same as input for global profiling run. Default is NULL.
annotation_protein	same as annotation for global profiling run. Default is NULL.
use_unmod_peptides	If protein_input is not provided, unmodified peptides can be extracted from input to be used in place of a global profiling run. Default is FALSE.
mod_ids	List of modifications of interest. Default is a list with only ⁠Common Biological:Phosphorylation on S⁠. Please note that the 'mod_ids' parameter currently supports lists of size 1 only. Future updates aim to extend its functionality to accommodate lists of greater sizes. Note ⁠\\⁠ must be included before special characters.
useUniquePeptide	TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
removeFewMeasurements	TRUE (default) will remove the features that have 1 or 2 measurements across runs.
removeProtein_with1Feature	TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
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.

Value

a list of two data.tables named 'PTM' and 'PROTEIN' in the format required by MSstatsPTM.

Author(s)

Anthony Wu

Examples

input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", 
                                package = "MSstatsPTM")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv", 
                                package = "MSstatsPTM")
annot = data.table::fread(annot)
input_protein = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaksGlobalProteome.tsv",
                                package = "MSstatsPTM")
input_protein = data.table::fread(input_protein)
annot_protein = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesignGlobalProteome.tsv", 
                                package = "MSstatsPTM")
annot_protein = data.table::fread(annot_protein)
fasta_path=system.file("extdata", "metamorpheus_fasta.fasta", 
                                package="MSstatsPTM")
metamorpheus_imported = MetamorpheusToMSstatsPTMFormat(
    input, 
    annot, 
    fasta_path=fasta_path,
    input_protein=input_protein,
    annotation_protein=annot_protein,
    use_unmod_peptides=FALSE,
    mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
)
head(metamorpheus_imported$PTM)
head(metamorpheus_imported$PROTEIN)

Vitek-Lab/MSstatsPTM documentation built on Dec. 19, 2024, 6:02 a.m.