MSstatsClean: Clean files generated by a signal processing tools.

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

Clean files generated by a signal processing tools.

Description

Clean files generated by a signal processing tools.

Clean DIAUmpire files

Clean MaxQuant files

Clean OpenMS files

Clean OpenSWATH files

Clean Progenesis files

Clean ProteomeDiscoverer files

Clean Skyline files

Clean SpectroMine files

Clean Spectronaut files

Clean Philosopher files

Clean DIA-NN files

Clean Metamorpheus files

Clean Protein Prospector files

Usage

MSstatsClean(msstats_object, ...)

## S4 method for signature 'MSstatsDIAUmpireFiles'
MSstatsClean(msstats_object, use_frag, use_pept)

## S4 method for signature 'MSstatsMaxQuantFiles'
MSstatsClean(
  msstats_object,
  protein_id_col,
  remove_by_site = FALSE,
  channel_columns = "Reporterintensitycorrected"
)

## S4 method for signature 'MSstatsOpenMSFiles'
MSstatsClean(msstats_object)

## S4 method for signature 'MSstatsOpenSWATHFiles'
MSstatsClean(msstats_object)

## S4 method for signature 'MSstatsProgenesisFiles'
MSstatsClean(msstats_object, runs, fix_colnames = TRUE)

## S4 method for signature 'MSstatsProteomeDiscovererFiles'
MSstatsClean(
  msstats_object,
  quantification_column,
  protein_id_column,
  sequence_column,
  remove_shared,
  remove_protein_groups = TRUE,
  intensity_columns_regexp = "Abundance"
)

## S4 method for signature 'MSstatsSkylineFiles'
MSstatsClean(msstats_object)

## S4 method for signature 'MSstatsSpectroMineFiles'
MSstatsClean(msstats_object)

## S4 method for signature 'MSstatsSpectronautFiles'
MSstatsClean(msstats_object, intensity)

## S4 method for signature 'MSstatsPhilosopherFiles'
MSstatsClean(
  msstats_object,
  protein_id_col,
  peptide_id_col,
  channels,
  remove_shared_peptides
)

## S4 method for signature 'MSstatsDIANNFiles'
MSstatsClean(
  msstats_object,
  MBR = TRUE,
  quantificationColumn = "FragmentQuantCorrected"
)

## S4 method for signature 'MSstatsMetamorpheusFiles'
MSstatsClean(msstats_object)

## S4 method for signature 'MSstatsProteinProspectorFiles'
MSstatsClean(msstats_object)

Arguments

msstats_object	object that inherits from MSstatsInputFiles class.
...	additional parameter to specific cleaning functions.
use_frag	TRUE will use the selected fragment for each peptide. 'Selected_fragments' column is required.
use_pept	TRUE will use the selected fragment for each protein 'Selected_peptides' column is required.
protein_id_col	character, name of a column with names of proteins.
remove_by_site	logical, if TRUE, proteins only identified by site will be removed.
channel_columns	character, regular expression that identifies channel columns in TMT data.
runs	chr, vector of Run labels.
fix_colnames	lgl, if TRUE, one of the rows will be used as colnames.
quantification_column	chr, name of a column used for quantification.
protein_id_column	chr, name of a column with protein IDs.
sequence_column	chr, name of a column with peptide sequences.
remove_shared	lgl, if TRUE, shared peptides will be removed.
remove_protein_groups	if TRUE, proteins with numProteins > 1 will be removed.
intensity_columns_regexp	regular expressions that defines intensity columns. Defaults to "Abundance", which means that columns that contain the word "Abundance" will be treated as corresponding to intensities for different channels.
intensity	chr, specifies which column will be used for Intensity.
peptide_id_col	character name of a column that identifies peptides
channels	character vector of channel labels
remove_shared_peptides	logical, if TRUE, shared peptides will be removed based on the IsUnique column from Philosopher output
MBR	True if analysis was done with match between runs
quantificationColumn	Use 'FragmentQuantCorrected'(default) column for quantified intensities. 'FragmentQuantRaw' can be used instead.

Value

data.table

data.table

data.table

data.table

data.table

data.table

data.table

data.table

data.table

data.table

data.table

data.table

data.table

Examples

evidence_path = system.file("tinytest/raw_data/MaxQuant/mq_ev.csv", 
                            package = "MSstatsConvert")
pg_path = system.file("tinytest/raw_data/MaxQuant/mq_pg.csv", 
                      package = "MSstatsConvert")
evidence = read.csv(evidence_path)
pg = read.csv(pg_path)
imported = MSstatsImport(list(evidence = evidence, protein_groups = pg),
                         "MSstats", "MaxQuant")
cleaned_data = MSstatsClean(imported, protein_id_col = "Proteins")
head(cleaned_data)

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