groupComparisonTMTPTM {MSstatsTMTPTM} | R Documentation

## Model PTM and/or protein data and make adjustments if needed

### Description

Takes summarized PTM data from proteinSummarization and models with groupComparisonTMT. Can also take protein level data in the same format and model with groupComparisonTMT. Including protein data allows for adjusting PTM Fold Change by the change in protein abundance without modification.

### Usage

    groupComparisonTMTPTM(
      data.ptm,
      data.protein = NULL,
      contrast.matrix = "pairwise",
      moderated = FALSE,
      adj.method = "BH"
    )

### Arguments

`data.ptm` | Name of the output of the MSstatsTMT `proteinSummarization` function with PTM data. It should have columns named `Protein`, `TechRepMixture`, `Mixture`, `Run`, `Channel`, `Condition`, `BioReplicate`, `Abundance`.
`data.protein` | Protein dataset returned by the MSstatsTMT `proteinSummarization` function
`contrast.matrix` | Comparison between conditions of interests. 1) default is 'pairwise', which compare all possible pairs between two conditions. 2) Otherwise, users can specify the comparisons of interest. Based on the levels of conditions, specify 1 or -1 to the conditions of interests and 0 otherwise. The levels of conditions are sorted alphabetically.
`moderated` | TRUE will moderate t statistic; FALSE (default) uses ordinary t statistic.
`adj.method` | Adjusted method for multiple comparison. "BH" is default.

### Value

A list `models` of all modeled and adjusted datasets

### Examples

    # Load summarized datasets from MSstatsTMT proteinSummarization function
    data(quant.msstats.ptm)
    data(quant.msstats.protein)

    # Load specific contrast matrix
    data(example.contrast.matrix)

    model.results.contrast <- groupComparisonTMTPTM(data.ptm=quant.msstats.ptm,
                                          data.protein=quant.msstats.protein,
                                          contrast.matrix = example.contrast.matrix)

[Package MSstatsTMTPTM version 1.1.2 Index]