MSstatsSummarizationOutput: Post-processing output from MSstats summarization

View source: R/utils_output.R

MSstatsSummarizationOutputR 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)


MeenaChoi/MSstats documentation built on July 13, 2024, 10:59 a.m.