OpenMStoMSstatsTMTFormat {MSstatsTMT} | R Documentation |
Convert OpenMS MSstatsTMT report into the required input format for MSstatsTMT.
OpenMStoMSstatsTMTFormat( input, useUniquePeptide = TRUE, rmPSM_withMissing_withinRun = FALSE, rmPSM_withfewMea_withinRun = TRUE, rmProtein_with1Feature = FALSE, summaryforMultiplePSMs = sum )
input |
MSstatsTMT report from OpenMS |
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. |
summaryforMultiplePSMs |
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.om) input.om <- OpenMStoMSstatsTMTFormat(raw.om) head(input.om)