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 1.6.6 Index]