MSstatsGroupComparison {MSstats} | R Documentation

## Group comparison

### Description

Group comparison

### Usage

    MSstatsGroupComparison(
      summarized_list,
      contrast_matrix,
      save_fitted_models,
      repeated,
      samples_info
    )

### Arguments

`summarized_list` | output of MSstatsPrepareForGroupComparison
`contrast_matrix` | contrast matrix
`save_fitted_models` | if TRUE, fitted models will be included in the output
`repeated` | logical, output of checkRepeatedDesign function
`samples_info` | data.table, output of getSamplesInfo function

### Examples

    QuantData <- dataProcess(SRMRawData, use_log_file = FALSE)
    group_comparison_input = MSstatsPrepareForGroupComparison(QuantData)
    levels(QuantData$ProteinLevelData$GROUP)
    comparison <- matrix(c(-1,0,0,0,0,0,1,0,0,0),nrow=1)
    row.names(comparison) <- "T7-T1"
    groups = levels(QuantData$ProteinLevelData$GROUP)
    colnames(comparison) <- groups[order(as.numeric(groups))]
    samples_info = getSamplesInfo(QuantData)
    repeated = checkRepeatedDesign(QuantData)
    group_comparison = MSstatsGroupComparison(group_comparison_input, comparison,
                                              FALSE, repeated, samples_info)
    length(group_comparison) # list of length equal to number of proteins
    group_comparison[[1]][[1]] # data used to fit linear model
    group_comparison[[1]][[2]] # comparison result
    group_comparison[[2]][[3]] # NULL, because we set save_fitted_models to FALSE

[Package MSstats version 4.1.1 Index]