groupComparisonPTM {MSstatsPTM} | R Documentation

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

### Description

Takes summarized PTM and protein data from proteinSummarization. If protein data is unavailable, PTM data only can be passed into the function. Including protein data allows for adjusting PTM Fold Change by the change in protein abundance without modification. MSstatsContrastMatrix

### Usage

    groupComparisonPTM(
      data,
      data.type,
      contrast.matrix = "pairwise",
      moderated = FALSE,
      adj.method = "BH",
      log_base = 2,
      use_log_file = TRUE,
      append = FALSE,
      verbose = TRUE,
      log_file_path = NULL,
      base = "MSstatsPTM_log_"
    )

### Arguments

`data` | list of summarized datasets. Output of MSstatsPTM summarization function `dataSummarizationPTM` or `dataSummarizationPTM_TMT` depending on acquisition type.
`data.type` | string indicating experimental acquisition type. "TMT" is used for TMT labeled experiments. For all other experiments (Label Free/ DDA/ DIA) use "LabelFree".
`contrast.matrix` | comparison between conditions of interests. Default models full pairwise comparison between all conditions
`moderated` | For TMT experiments only. TRUE will moderate t statistic; FALSE (default) uses ordinary t statistic. Default is FALSE.
`adj.method` | For TMT experiemnts only. Adjusted method for multiple comparison. "BH" is default. "BH" is used for all other experiment types
`log_base` | For non-TMT experiments only. The base of the logarithm used in summarization.
`use_log_file` | logical. If TRUE, information about data processing will be saved to a file.
`append` | logical. If TRUE, information about data processing will be added to an existing log file.
`verbose` | logical. If TRUE, information about data processing will be printed to the console.
`log_file_path` | character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If `append = TRUE`, has to be a valid path to a file.
`base` | start of the file name.

### Value

list of modeling results. Includes PTM, PROTEIN, and ADJUSTED data.tables with their corresponding model results.

### Examples

    model.lf.msstatsptm <- groupComparisonPTM(summary.data,
                                         data.type = "LabelFree",
                                         verbose = FALSE)

[Package MSstatsPTM version 1.4.2 Index]