OpenMStoMSstatsTMTFormat {MSstatsTMT}R Documentation

Generate MSstatsTMT required input format for OpenMS output

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)

[Package MSstatsTMT version 1.8.2 Index]