PhilosophertoMSstatsTMTFormat: Convert Philosopher (Fragpipe) 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 Philosopher (Fragpipe) output to MSstatsTMT format.

Description

Convert Philosopher (Fragpipe) output to MSstatsTMT format.

Usage

PhilosophertoMSstatsTMTFormat(
  input,
  annotation,
  protein_id_col = "Protein",
  peptide_id_col = "Peptide.Sequence",
  Purity_cutoff = 0.6,
  PeptideProphet_prob_cutoff = 0.7,
  useUniquePeptide = TRUE,
  rmPSM_withfewMea_withinRun = TRUE,
  rmPeptide_OxidationM = TRUE,
  rmProtein_with1Feature = FALSE,
  summaryforMultipleRows = sum,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

input	data.frame of 'msstats.csv' file produced by Philosopher
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. Channel column should be consistent with the channel columns (Ignore the prefix "Channel ") in msstats.csv file. Run column should be consistent with the Spectrum.File columns in msstats.csv file.
protein_id_col	Use 'Protein'(default) column for protein name. 'Master.Protein.Accessions' can be used instead to get the protein ID with single protein.
peptide_id_col	Use 'Peptide.Sequence'(default) column for peptide sequence. 'Modified.Peptide.Sequence' can be used instead to get the modified peptide sequence.
Purity_cutoff	Cutoff for purity. Default is 0.6
PeptideProphet_prob_cutoff	Cutoff for the peptide identification probability. Default is 0.7. The probability is confidence score determined by PeptideProphet and higher values indicate greater confidence.
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.
rmPeptide_OxidationM	TRUE (default) will remove the peptides including oxidation (M) sequence.
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'

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