MSstatsSummarizationOutput {MSstats} | R Documentation

## Post-processing output from MSstats summarization

### Description

Post-processing output from MSstats summarization

### Usage

    MSstatsSummarizationOutput(
      input,
      summarized,
      processed,
      method,
      impute,
      censored_symbol
    )

### Arguments

`input` | 'data.table' in MSstats format
`summarized` | output of the 'MSstatsSummarize' function
`processed` | output of MSstatsSelectFeatures
`method` | name of the summarization method ('summaryMethod' parameter to 'dataProcess')
`impute` | if TRUE, censored missing values were imputed ('MBimpute' parameter to 'dataProcess')
`censored_symbol` | censored missing value indicator ('censoredInt' parameter to 'dataProcess')

### Value

list that consists of the following elements:

- FeatureLevelData - feature-level data after processing

- ProteinLevelData - protein-level (summarized) data

- SummaryMethod (string) - name of summarization method that was used

### Examples

    raw = DDARawData
    method = "TMP"
    cens = "NA"
    impute = TRUE
    MSstatsConvert::MSstatsLogsSettings(FALSE)
    input = MSstatsPrepareForDataProcess(raw, 2, NULL)
    input = MSstatsNormalize(input, "EQUALIZEMEDIANS")
    input = MSstatsMergeFractions(input)
    input = MSstatsHandleMissing(input, "TMP", TRUE, "NA", 0.999)
    input = MSstatsSelectFeatures(input, "all")
    processed = getProcessed(input)
    input = MSstatsPrepareForSummarization(input, method, impute, cens, FALSE)
    input_split = split(input, input$PROTEIN)
    summarized = MSstatsSummarize(input_split, method, impute, cens, FALSE, TRUE)
    output = output = MSstatsSummarizationOutput(input, summarized, processed,
    method, impute, cens)

[Package MSstats version 4.0.1 Index]