MaxQtoMSstatsTMTFormat {MSstatsTMT} | R Documentation |
Convert MaxQuant output into the required input format for MSstatsTMT.
MaxQtoMSstatsTMTFormat(evidence, proteinGroups, annotation, fraction = FALSE, which.proteinid = "Proteins", rmProt_Only.identified.by.site = FALSE, useUniquePeptide = TRUE, rmPSM_withMissing_withinRun = FALSE, rmPSM_withfewMea_withinRun = TRUE, rmProtein_with1Feature = FALSE, summaryforMultipleRows = sum)
evidence |
name of 'evidence.txt' data, which includes feature-level data. |
proteinGroups |
name of 'proteinGroups.txt' data. |
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 'Proteins'(default) column for protein name. 'Leading.proteins' or 'Leading.razor.proteins' can be used instead. However, those can potentially have the shared peptides. |
rmProt_Only.identified.by.site |
TRUE will remove proteins with '+' in 'Only.identified.by.site' column from proteinGroups.txt, which was identified only by a modification site. FALSE is the default. |
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(evidence) head(proteinGroups) head(annotation.mq) input.mq <- MaxQtoMSstatsTMTFormat(evidence, proteinGroups, annotation.mq) head(input.mq)