MSstatsGroupComparisonSingleProtein {MSstats} | R Documentation

## Group comparison for a single protein

### Description

Group comparison for a single protein

### Usage

    MSstatsGroupComparisonSingleProtein(
      single_protein,
      contrast_matrix,
      repeated,
      groups,
      samples_info,
      save_fitted_models,
      has_imputed
    )

### Arguments

`single_protein` | data.table with summarized data for a single protein
`contrast_matrix` | contrast matrix
`repeated` | if TRUE, repeated measurements will be modeled
`groups` | unique labels of experimental conditions
`samples_info` | number of runs per group
`save_fitted_models` | if TRUE, fitted model will be saved. If not, it will be replaced with NULL
`has_imputed` | TRUE if missing values have been imputed

### 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)
    single_output <- MSstatsGroupComparisonSingleProtein(
      group_comparison_input[[1]], comparison, repeated, groups, samples_info,
      FALSE, TRUE)
    single_output # same as a single element of MSstatsGroupComparison output

[Package MSstats version 4.1.1 Index]