getProcessed {MSstats} | R Documentation

## Get feature-level data to be used in the MSstatsSummarizationOutput function

### Description

Get feature-level data to be used in the MSstatsSummarizationOutput function

### Usage

    getProcessed(input)

### Arguments

`input` | data.table processed by dataProcess subfunctions

### Value

data.table processed by dataProcess subfunctions

### 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_all = MSstatsSelectFeatures(input, "all") # all features
    input_5 = MSstatsSelectFeatures(data.table::copy(input),
    "topN", top_n = 5) # top 5 features

    proc1 = getProcessed(input_all)
    proc2 = getProcessed(input_5)

    proc1
    proc2

[Package MSstats version 4.1.1 Index]