PDtoMSstatsTMTFormat {MSstatsTMT} | R Documentation |
Convert Proteome Discoverer output to MSstatsTMT format.
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, ... )
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'. |
'data.frame' of class 'MSstatsTMT'
head(raw.pd) head(annotation.pd) input.pd <- PDtoMSstatsTMTFormat(raw.pd, annotation.pd) head(input.pd)