groupComparisonLiP {MSstatsLiP} | R Documentation

## Model LiP and TrP data and make adjustments if needed Returns list of three modeled datasets

### Description

Takes summarized LiP peptide and TrP protein data from dataSummarizationLiP If global protein data is unavailable, LiP data only can be passed into the function. Including protein data allows for adjusting LiP Fold Change by the change in global protein abundance..

### Usage

    groupComparisonLiP(
      data,
      contrast.matrix = "pairwise",
      fasta.path = NULL,
      log_base = 2,
      use_log_file = FALSE,
      append = FALSE,
      verbose = TRUE,
      log_file_path = NULL,
      base = "MSstatsLiP_log_"
    )

### Arguments

`data` | list of summarized datasets. Can be output of MSstatsLiP summarization function `dataSummarizationLiP`. Must include dataset named "LiP" as minimum.
`contrast.matrix` | comparison between conditions of interests. Default models full pairwise comparison between all conditions
`fasta.path` | a file path to a fasta file that includes the proteins listed in the data. Default is NULL. Include this parameter to determine trypticity of peptides in LiP models.
`log_base` | base of the logarithm used in dataProcess.
`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 LiP, PROTEIN, and ADJUSTED LiP data.tables with their corresponding model results.

### Examples

    ## Use output of dataSummarizationLiP function
    fasta <- system.file("extdata", "ExampleFastaFile.fasta", package="MSstatsLiP")

    # Test for pairwise comparison
    MSstatsLiP_model <- groupComparisonLiP(MSstatsLiP_Summarized,
                                       contrast.matrix = "pairwise",
                                       fasta.path = fasta)

    # Returns list of three models
    names(MSstatsLiP_model)
    head(MSstatsLiP_model$LiP.Model)
    head(MSstatsLiP_model$TrP.Model)
    head(MSstatsLiP_model$Adjusted.LiP.Model)

[Package MSstatsLiP version 1.0.0 Index]