PDtoMSstatsTMTFormat {MSstatsTMT} | R Documentation

## Generate MSstatsTMT required input format from Proteome discoverer output

### Description

Convert Proteome discoverer output into the required input format for MSstatsTMT.

### Usage

    PDtoMSstatsTMTFormat(
      input,
      annotation,
      which.proteinid = "Protein.Accessions",
      useNumProteinsColumn = TRUE,
      useUniquePeptide = TRUE,
      rmPSM_withMissing_withinRun = FALSE,
      rmPSM_withfewMea_withinRun = TRUE,
      rmProtein_with1Feature = FALSE,
      summaryforMultipleRows = sum
    )

### Arguments

`input` | data name of Proteome discover PSM output.
`annotation` | data frame which contains column Run, Fraction, TechRepMixture, Mixture, Channel, BioReplicate, Condition. Refer to the example 'annotation.pd' for the meaning of each column.
`which.proteinid` | Use 'Protein.Accessions'(default) column for protein name. 'Master.Protein.Accessions' can be used instead to get the protein name with single protein.
`useNumProteinsColumn` | TURE(default) remove shared peptides by information of # Proteins column in PSM sheet.
`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.

### Value

input for `proteinSummarization` function

### Examples

    head(raw.pd)
    head(annotation.pd)
    input.pd <- PDtoMSstatsTMTFormat(raw.pd, annotation.pd)
    head(input.pd)

[Package MSstatsTMT version 1.4.6 Index]