OpenMStoMSstatsTMTFormat: Generate MSstatsTMT required input format for OpenMS output

In MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Description

Convert OpenMS MSstatsTMT report into the required input format for MSstatsTMT.

Usage

OpenMStoMSstatsTMTFormat(
  input,
  useUniquePeptide = TRUE,
  rmPSM_withMissing_withinRun = FALSE,
  rmPSM_withfewMea_withinRun = TRUE,
  rmProtein_with1Feature = FALSE,
  summaryforMultiplePSMs = sum
)

Arguments

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.

Value

input for proteinSummarization function

Examples

head(raw.om)
input.om <- OpenMStoMSstatsTMTFormat(raw.om)
head(input.om)

MSstatsTMT documentation built on Dec. 20, 2020, 2:01 a.m.