MSstatsSummarizationOutput: Post-processing output from MSstats summarization

In Vitek-Lab/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

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)

Vitek-Lab/MSstats documentation built on April 21, 2024, 10:14 p.m.