PDtoMSstatsTMTFormat {MSstatsTMT} | R Documentation

## Generate MSstatsTMT required input format for Proteome discoverer output

### Description

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

### Usage

    PDtoMSstatsTMTFormat(input, annotation, fraction = FALSE,
      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, Channel, Condition, BioReplicate, Mixture.
`fraction` | indicates whether the data has fractions. If there are fractions, then overlapped peptide ions will be removed and then fractions are combined for each mixture.
`which.proteinid` | Use 'Protein.Accessions'(default) column for protein name. 'Master.Protein.Accessions' can be used instead.
`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 1.1.2 Index]