MSstatsSummarizationOutput {MSstats} | R Documentation |
Post-processing output from MSstats summarization
MSstatsSummarizationOutput( input, summarized, processed, method, impute, censored_symbol )
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') |
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
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)