Post-processing output from MSstats summarization

Post-processing output from MSstats summarization

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)
#> INFO  [2021-07-05 20:05:29] ** Features with one or two measurements across runs are removed.
#> INFO  [2021-07-05 20:05:29] ** Fractionation handled.
#> INFO  [2021-07-05 20:05:29] ** Updated quantification data to make balanced design. Missing values are marked by NA
input = MSstatsNormalize(input, "EQUALIZEMEDIANS")
input = MSstatsMergeFractions(input)
input = MSstatsHandleMissing(input, "TMP", TRUE, "NA", 0.999)
#> INFO  [2021-07-05 20:05:29] ** Log2 intensities under cutoff = 13.456  were considered as censored missing values.
#> INFO  [2021-07-05 20:05:29] ** Log2 intensities = NA were considered as censored missing values.
input = MSstatsSelectFeatures(input, "all")
#> INFO  [2021-07-05 20:05:29] ** Use all features that the dataset originally has.
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)
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |============                                                          |  17%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |==========================================================            |  83%
  |                                                                            
  |======================================================================| 100%
output = output = MSstatsSummarizationOutput(input, summarized, processed,
method, impute, cens)