MSstatsGroupComparisonOutput {MSstats} | R Documentation

## Create output of group comparison based on results for individual proteins

### Description

Create output of group comparison based on results for individual proteins

### Usage

    MSstatsGroupComparisonOutput(input, summarization_output, log_base = 2)

### Arguments

`input` | output of MSstatsGroupComparison function
`summarization_output` | output of dataProcess function
`log_base` | base of the logarithm used in fold-change calculation

### Value

list, same as the output of 'groupComparison'

### 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)
    group_comparison_final = MSstatsGroupComparisonOutput(group_comparison,
                                                          QuantData)
    group_comparison_final[["ComparisonResult"]]

[Package MSstats version 4.0.1 Index]