MaxQtoMSstatsTMTFormat {MSstatsTMT} | R Documentation

## Generate MSstatsTMT required input format from MaxQuant output

### Description

Convert MaxQuant output into the required input format for MSstatsTMT.

### Usage

    MaxQtoMSstatsTMTFormat(
      evidence,
      proteinGroups,
      annotation,
      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, Fraction, TechRepMixture, Mixture, Channel, BioReplicate, Condition. Refer to the example 'annotation.mq' for the meaning of each column.
`which.proteinid` | Use 'Proteins'(default) column for protein name. 'Leading.proteins' or 'Leading.razor.proteins' or 'Gene.names' can be used instead to get the protein ID with single protein. 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 1.6.6 Index]