% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/main_calculations.R
 \name{tmt_summarization_loop}
 \alias{tmt_summarization_loop}
 \title{Main TMT summarization calculation function for MSstatsShiny application}
 \usage{

 tmt_summarization_loop(data, qc_input, loadpage_input, busy_indicator = TRUE)

 }
 \arguments{
 \item{data}{Data converted into MSstats format.}
 

 \item{qc_input}{options for data processing input by the user from data processing page.}
 
 \item{loadpage_input}{options for data processing input by the user from data upload page.}

 
 \item{busy_indicator}{Boolean indicator indicating whether or not to display
 shiny waiting indicator.}

 }
 \value{
 list of TMT summarization results
 }
 \description{
 Main TMT function to calculate MSstatsShiny results.
 }

 \examples{
 data(raw.pd, package = "MSstatsTMT")
 data(annotation.pd, package = "MSstatsTMT")
 
 testdata <- MSstatsTMT::PDtoMSstatsTMTFormat(raw.pd, 
                                              annotation.pd,
                                              use_log_file = FALSE
                                              )
 
 qc_input = list()
 loadpage_input = list()
 qc_input$summarization = "msstats"
 qc_input$norm = "equalizeMedians"
 qc_input$log = 2
 qc_input$names = NULL
 qc_input$features_used	= "all"
 code_n_feat=3
 qc_input$censInt = "NA"
 qc_input$MBi = TRUE
 qc_input$remove50 = FALSE
 qc_input$maxQC = 0.999
 qc_input$null = FALSE
 qc_input$null1 = FALSE
 loadpage_input$DDA_DIA = "LF"
 qc_input$global_norm = TRUE
 qc_input$reference_norm = TRUE
 qc_input$remove_norm_channel = TRUE
 qc_input$maxQC1 = NULL
 summarization_tmt_test = tmt_summarization_loop(testdata, qc_input,loadpage_input, 
                                                busy_indicator = FALSE)
 
 }