View source: R/utils_summarization_prepare.R
getProcessed | R Documentation |
Get feature-level data to be used in the MSstatsSummarizationOutput function
getProcessed(input)
input |
data.table processed by dataProcess subfunctions |
data.table processed by dataProcess subfunctions
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
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