PDtoMSstatsTMTFormat {MSstatsTMT} | R Documentation |
Convert Proteome discoverer output into the required input format for MSstatsTMT.
PDtoMSstatsTMTFormat(input, annotation, fraction = FALSE, which.proteinid = "Protein.Accessions", useNumProteinsColumn = TRUE, useUniquePeptide = TRUE, rmPSM_withMissing_withinRun = FALSE, rmPSM_withfewMea_withinRun = TRUE, rmProtein_with1Feature = FALSE, summaryforMultipleRows = sum)
input |
data name of Proteome discover PSM output. |
annotation |
data frame which contains column Run, Channel, Condition, BioReplicate, Mixture. |
fraction |
indicates whether the data has fractions. If there are fractions, then overlapped peptide ions will be removed and then fractions are combined for each mixture. |
which.proteinid |
Use 'Protein.Accessions'(default) column for protein name. 'Master.Protein.Accessions' can be used instead. |
useNumProteinsColumn |
TURE(default) remove shared peptides by information of # Proteins column in PSM sheet. |
useUniquePeptide |
TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein. |
rmPSM_withMissing_withinRun |
TRUE will remove PSM with any missing value within each Run. Defaut is FALSE. |
rmPSM_withfewMea_withinRun |
only for rmPSM_withMissing_withinRun = FALSE. 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. |
input for proteinSummarization
function
head(raw.pd) head(annotation.pd) input.pd <- PDtoMSstatsTMTFormat(raw.pd, annotation.pd) head(input.pd)