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

MSstatsClean(msstats_object, ...)

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

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

# S4 method for MSstatsOpenMSFiles
MSstatsClean(msstats_object)

# S4 method for MSstatsOpenSWATHFiles
MSstatsClean(msstats_object)

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

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

# S4 method for MSstatsSkylineFiles
MSstatsClean(msstats_object)

# S4 method for MSstatsSpectroMineFiles
MSstatsClean(msstats_object)

# S4 method for MSstatsSpectronautFiles
MSstatsClean(msstats_object, intensity)

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.

Value

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")
#> INFO  [2021-05-10 23:03:41] ** Raw data from MaxQuant imported successfully.
cleaned_data = MSstatsClean(imported, protein_id_col = "Proteins")
#> INFO  [2021-05-10 23:03:41] ** Rows with values of Potentialcontaminant equal to + are removed 
#> INFO  [2021-05-10 23:03:41] ** Rows with values of Reverse equal to + are removed 
#> INFO  [2021-05-10 23:03:41] ** Rows with values of Potentialcontaminant equal to + are removed 
#> INFO  [2021-05-10 23:03:41] ** Rows with values of Reverse equal to + are removed 
#> INFO  [2021-05-10 23:03:41] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
#> INFO  [2021-05-10 23:03:41] ** Raw data from MaxQuant cleaned successfully.
head(cleaned_data)
#>    ProteinName PeptideSequence Modifications PrecursorCharge
#> 1:      P06959     AEAPAAAPAAK    Unmodified               2
#> 2:      P06959     AEAPAAAPAAK    Unmodified               2
#> 3:      P06959     AEAPAAAPAAK    Unmodified               2
#> 4:      P06959     AEAPAAAPAAK    Unmodified               2
#> 5:      P06959     AEAPAAAPAAK    Unmodified               2
#> 6:      P06959     AEAPAAAPAAK    Unmodified               2
#>                                            Run Intensity   Score
#> 1: 121219_S_CCES_01_01_LysC_Try_1to10_Mixt_1_1   4023100  76.332
#> 2: 121219_S_CCES_01_02_LysC_Try_1to10_Mixt_1_2   5132500  83.081
#> 3: 121219_S_CCES_01_03_LysC_Try_1to10_Mixt_1_3   2761600 104.430
#> 4: 121219_S_CCES_01_05_LysC_Try_1to10_Mixt_2_2   4091800  94.465
#> 5: 121219_S_CCES_01_06_LysC_Try_1to10_Mixt_2_3   4727000  88.596
#> 6: 121219_S_CCES_01_08_LysC_Try_1to10_Mixt_3_2   2258400  90.050

Clean files generated by a signal processing tools.

Arguments

Value

Examples

Contents