ProteinProspectortoMSstatsTMTFormat: Generate MSstatsTMT required input format from Protein...

In Vitek-Lab/MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

Generate MSstatsTMT required input format from Protein Prospector output

Description

Generate MSstatsTMT required input format from Protein Prospector output

Usage

ProteinProspectortoMSstatsTMTFormat(
  input,
  annotation,
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeProtein_with1Feature = FALSE,
  summaryforMultipleRows = sum,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL
)

Arguments

input	txt report file from Protein Prospector with ⁠Keep Replicates⁠ option selected.
annotation	data frame which contains column Run, Fraction, TechRepMixture, Mixture, Channel, BioReplicate, Condition.
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

data.frame of class "MSstatsTMT"

Examples

input = system.file("tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt",
    package = "MSstatsConvert")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv",
                                package = "MSstatsConvert")
annot = data.table::fread(annot)
output <- ProteinProspectortoMSstatsTMTFormat(input, annot)
head(output)

Vitek-Lab/MSstatsConvert documentation built on Dec. 17, 2024, 1:14 a.m.