PDtoMSstatsTMTFormat: Convert Proteome Discoverer output to MSstatsTMT format.

In Vitek-Lab/MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Convert Proteome Discoverer output to MSstatsTMT format.

Description

Convert Proteome Discoverer output to MSstatsTMT format.

Usage

PDtoMSstatsTMTFormat(
  input,
  annotation,
  which.proteinid = "Protein.Accessions",
  useNumProteinsColumn = TRUE,
  useUniquePeptide = TRUE,
  rmPSM_withfewMea_withinRun = TRUE,
  rmProtein_with1Feature = FALSE,
  summaryforMultipleRows = sum,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

input	PD report or a path to it.
annotation	annotation with Run, Fraction, TechRepMixture, Mixture, Channel, BioReplicate, Condition columns or a path to file. Refer to the example 'annotation' for the meaning of each column.
which.proteinid	Use 'Protein.Accessions'(default) column for protein name. 'Master.Protein.Accessions' can be used instead to get the protein name with single protein.
useNumProteinsColumn	logical, TURE(default) remove shared peptides by information of # Proteins column in PSM sheet.
useUniquePeptide	logical, if TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
rmPSM_withfewMea_withinRun	TRUE (default) will remove the features that have 1 or 2 measurements within each Run.
rmProtein_with1Feature	TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.
summaryforMultipleRows	sum (default) or max - when there are multiple measurements for certain feature in certain run, select the feature with the largest summation or maximal value.
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' of class 'MSstatsTMT'

Examples

head(raw.pd)
head(annotation.pd)
input.pd <- PDtoMSstatsTMTFormat(raw.pd, annotation.pd)
head(input.pd)

Vitek-Lab/MSstatsTMT documentation built on April 30, 2024, 6:05 p.m.