MaxQtoMSstatsTMTFormat {MSstatsTMT} | R Documentation

## Generate MSstatsTMT required input format for MaxQuant output

### Description

Convert MaxQuant output into the required input format for MSstatsTMT.

### Usage

    MaxQtoMSstatsTMTFormat(evidence, proteinGroups, annotation, fraction = FALSE,
      which.proteinid = "Proteins", rmProt_Only.identified.by.site = FALSE,
      useUniquePeptide = TRUE, rmPSM_withMissing_withinRun = FALSE,
      rmPSM_withfewMea_withinRun = TRUE, rmProtein_with1Feature = FALSE,
      summaryforMultipleRows = sum)

### Arguments

`evidence` | name of 'evidence.txt' data, which includes feature-level data.
`proteinGroups` | name of 'proteinGroups.txt' data.
`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 'Proteins'(default) column for protein name. 'Leading.proteins' or 'Leading.razor.proteins' can be used instead. However, those can potentially have the shared peptides.
`rmProt_Only.identified.by.site` | TRUE will remove proteins with '+' in 'Only.identified.by.site' column from proteinGroups.txt, which was identified only by a modification site. FALSE is the default.
`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(evidence)
    head(proteinGroups)
    head(annotation.mq)
    input.mq <- MaxQtoMSstatsTMTFormat(evidence, proteinGroups, annotation.mq)
    head(input.mq)

[Package MSstatsTMT version 1.1.2 Index]