@@ -9,7 +9,6 @@ export(lf_summarization_loop)

 export(radioTooltip)

 export(tmt_model)

 export(tmt_summarization_loop)

-export(uiObject)

 export(xy_str)

 import(MSstats)

 import(MSstatsConvert)

@@ -18,6 +18,9 @@

 #' transitions in RawData. Variable Intensity is required to be original signal

 #' without any log transformation and can be specified as the peak of height 

 #' or the peak of  area under curve.

+#' @examples

+#' data(example_dia_skyline)

+#' head(example_dia_skyline)

 #'

 NULL

@@ -31,6 +34,9 @@ NULL

 #' @docType data

 #'

 #' @format data.frame

+#' @examples

+#' data(example_skyline_annotation)

+#' head(example_skyline_annotation)

 #'

 NULL

@@ -45,6 +51,9 @@ NULL

 #' @docType data

 #'

 #' @format list

+#' @examples

+#' data(dia_skyline_summarized)

+#' head(dia_skyline_summarized)

 #'

 NULL

@@ -60,6 +69,9 @@ NULL

 #' @docType data

 #'

 #' @format list

+#' @examples

+#' data(dia_skyline_model)

+#' head(dia_skyline_model)

 #'

 NULL

@@ -74,6 +86,9 @@ NULL

 #' @docType data

 #'

 #' @format list

+#' @examples

+#' data(tmt_pd_summarized)

+#' head(tmt_pd_summarized)

 #'

 NULL

@@ -89,5 +104,8 @@ NULL

 #' @docType data

 #'

 #' @format list

+#' @examples

+#' data(tmt_pd_model)

+#' head(tmt_pd_model)

 #'

 NULL

\ No newline at end of file

@@ -13,9 +13,8 @@

 #' @param testMode One of TRUE or FALSE indicating whether or not to run the

 #' application in test mode. Default is FALSE.

 #' @examples

-#' 

-#' ## To run app set launch_app=TRUE

 #' \dontrun{

+#' ## To run app set launch_app=TRUE

 #' launch_MSstatsShiny(launch_app=FALSE,testMode=FALSE)

 #' }

 launch_MSstatsShiny = function(launch_app=TRUE, 

@@ -12,6 +12,34 @@

 #' @param busy_indicator Boolean indicator indicating whether or not to display 

 #' shiny waiting indicator.

 #' @return list of LF Summarization results

+#' @examples

+#' data("example_dia_skyline")

+#' data("example_skyline_annotation")

+#' testdata = MSstats::SkylinetoMSstatsFormat(example_dia_skyline,

+#'                                             annotation = example_skyline_annotation,

+#'                                             filter_with_Qvalue = TRUE, 

+#'                                             qvalue_cutoff = 0.01, 

+#'                                             fewMeasurements="remove", 

+#'                                             removeProtein_with1Feature = TRUE,

+#'                                             use_log_file = FALSE)

+#' 

+#' ## Source app functionality

+#' qc_input = list()

+#' loadpage_input = list()

+#' 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"

+#' lf_summarization_loop(testdata, qc_input,loadpage_input, busy_indicator=FALSE)

+#' 

 lf_summarization_loop = function(data, qc_input,loadpage_input, busy_indicator = TRUE){

   if (busy_indicator){

     show_modal_progress_line() # show the modal window

@@ -96,6 +124,37 @@ lf_summarization_loop = function(data, qc_input,loadpage_input, busy_indicator =

 #' shiny waiting indicator.

 #' 

 #' @return list of TMT summarization 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)

+#' 

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

   MBimpute = FALSE ## Add option for MBimpute to server..

   MSstatsConvert::MSstatsLogsSettings(FALSE,

@@ -232,6 +291,16 @@ tmt_summarization_loop = function(data, qc_input,loadpage_input, busy_indicator

 #' shiny waiting indicator.

 #' 

 #' @return list of LF modeling results

+#' @examples

+#' data("dia_skyline_summarized")

+#' comparison <- matrix(c(1, -1, 0, 0, 0, 0, 0, 0, 0, 0),nrow=1)

+#' row.names(comparison) = "1 vs 128"

+#' colnames(comparison) = c("1", "128", "16", "2", "256", 

+#'                          "32", "4", "512", "64", "8")

+#' model_lf_test = lf_model(dia_skyline_summarized, comparison, 

+#'                          busy_indicator = FALSE)

+#' 

+#' 

 lf_model = function(data, contrast.matrix, busy_indicator = TRUE){

   proteins = as.character(unique(data$ProteinLevelData[, 'Protein']))

@@ -299,6 +368,46 @@ lf_model = function(data, contrast.matrix, busy_indicator = TRUE){

 #' shiny waiting indicator.

 #' 

 #' @return list of TMT modeling 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

+#' qc_input$moderated = FALSE

+#' 

+#' summarization_tmt_test = tmt_summarization_loop(testdata, qc_input, loadpage_input,

+#'                                                busy_indicator = FALSE)

+#'                                                

+#' comparison=matrix(c(-1,0,0,1),nrow=1)

+#' row.names(comparison) = "1-0.125"

+#' colnames(comparison) = c("0.125", "0.5", "0.667", "1")

+#' 

+#' model_tmt_test = tmt_model(summarization_tmt_test, qc_input, comparison, 

+#'                            busy_indicator = FALSE)

+#' 

 tmt_model = function(data, input, contrast.matrix, busy_indicator = TRUE){

   proteins = as.character(unique(data$ProteinLevelData[, 'Protein']))

@@ -366,6 +475,11 @@ tmt_model = function(data, input, contrast.matrix, busy_indicator = TRUE){

 #' @param protein_model output of MSstats modeling function modeling unmodified proteins

 #' 

 #' @return list of PTM modeling results

+#' @examples

+#' model = MSstatsPTM::groupComparisonPTM(MSstatsPTM::summary.data, 

+#'                                        data.type = "LabelFree")

+#' apply_adj(model$PTM.Model, model$PROTEIN.Model)

+#' 

 apply_adj = function(ptm_model, protein_model){

   Label = Site = NULL

@@ -406,6 +520,10 @@ apply_adj = function(ptm_model, protein_model){

 #' @param qc_input options for data processing input by the user from data processing page.

 #' @param loadpage_input options for data processing input by the user from data upload page.

 #' @return string

+#' @examples

+#' qc_input = list(null=TRUE)

+#' loadpage_input = list(null=TRUE)

+#' QC_check(qc_input,loadpage_input)

 QC_check = function(qc_input,loadpage_input) {

   if (qc_input$null == TRUE || qc_input$null1 == TRUE) {

     maxQC = NULL

@@ -434,6 +552,8 @@ QC_check = function(qc_input,loadpage_input) {

 #' @param trigger how should prompt be shown

 #' @param options additional options to pass to function

 #' @return HTML object

+#' @examples

+#' radioTooltip("testid", "test_choice", "test_title")

 radioTooltip = function(id, choice, title, placement = "bottom", 

                         trigger = "hover", options = NULL){

@@ -83,6 +83,11 @@

 #' @importFrom graphics image mtext par plot.new

 #' @importFrom stats dist hclust qt

 #' @importFrom utils read.table write.table

+#' @examples

+#' data("dia_skyline_model")

+#' groupComparisonPlots2(dia_skyline_model$ComparisonResult, type="VolcanoPlot",

+#'                       address=FALSE)

+#' 

 groupComparisonPlots2 = function(data=data,

                                  type=type,

                                  sig=0.05,

@@ -73,50 +73,4 @@ server <- function(input, output, session) {

   observeEvent(input$"home-Reset", {

     refresh()

   })

-}

-

-# shinyServer(function(input, output, session) {

-#   options(shiny.maxRequestSize=10000*1024^2)

-#   session$allowReconnect(TRUE)

-#   observe({

-#     toggleClass(condition = TRUE,

-#                 class = "disabled",

-#                 selector = "#tablist li a[data-value='Data processing']")

-#   })

-# 

-#   observeEvent(input$"statmodel-Design", {

-#     updateTabsetPanel(session = session, inputId = "tablist", selected = "Future")

-#   })

-#   observeEvent(input$"home-StartPipeline", {

-#     updateTabsetPanel(session = session, inputId = "tablist", selected = "Uploaddata")

-#   })

-# 

-#   loadpage_input <- loadpageServer("loadpage", parent_session = session)

-#   qc_input <- callModule(qcServer, "qc",session, reactive(loadpage_input))

-#   statmodel_input <- callModule(statmodelServer, "statmodel",session, reactive(loadpage_input),reactive(qc_input))

-#   callModule(expdesServer, "expdes",session, reactive(loadpage_input),reactive(qc_input),reactive(statmodel_input))

-#   observeEvent(input$proceed, {

-#     updateTabsetPanel(session = session, inputId = "tablist", selected = "Uploaddata")

-#   })

-# 

-#   # statmodel= reactiveFileReader(1000, session, "panels/statmodel-ui.R", source)

-#   # output$statmodel = renderUI(statmodel())

-#   # 

-#   observe({

-#     if(input$"loadpage-DDA_DIA" %in% c("TMT", "PTM")){

-#       hideTab(inputId = "tablist", target = "PQ")

-#       hideTab(inputId = "tablist", target = "Future")

-#     }

-# 

-#     if(!(input$"loadpage-DDA_DIA" %in% c("TMT", "PTM"))){

-#       showTab(inputId = "tablist", target = "PQ")

-#       showTab(inputId = "tablist", target = "Future")

-#     }

-#   })

-# 

-#   observeEvent(input$"home-Reset", {

-#     refresh()

-#   })

-#   

-# }

-# )

+}

\ No newline at end of file

@@ -58,7 +58,6 @@ color: black !important;

 #' }

 #' @rdname uiObject

 #' @importFrom shiny NS span

-#' @export 

 uiObject <- function() {

   ui = navbarPage(

     title = "MSstatsShiny",

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@@ -17,3 +17,8 @@ string

 \description{

 Quick QC value check for LF vs TMT

 }

+\examples{

+qc_input = list(null=TRUE)

+loadpage_input = list(null=TRUE)

+QC_check(qc_input,loadpage_input)

+}

@@ -17,3 +17,9 @@ list of PTM modeling results

 \description{

 Main PTM function to model MSstatsShiny data.

 }

+\examples{

+model = MSstatsPTM::groupComparisonPTM(MSstatsPTM::summary.data, 

+                                       data.type = "LabelFree")

+apply_adj(model$PTM.Model, model$PROTEIN.Model)

+

+}

@@ -14,3 +14,8 @@ Data includes one list with two data.tables named \code{ComparisonResult} and

 \code{ModelQC} provides a report on the quality control checks of each protein

 in the dataset.

 }

+\examples{

+data(dia_skyline_model)

+head(dia_skyline_model)

+

+}

@@ -13,3 +13,8 @@ Data includes one list with two data.tables named \code{FeatureLevelData} and

 shows the unsummarized feature level data. \code{ProteinLevelData} shows the data

 summarized up to the protein level and is used for modeling the data.

 }

+\examples{

+data(dia_skyline_summarized)

+head(dia_skyline_summarized)

+

+}

@@ -24,3 +24,8 @@ transitions in RawData. Variable Intensity is required to be original signal

 without any log transformation and can be specified as the peak of height

 or the peak of  area under curve.

 }

+\examples{

+data(example_dia_skyline)

+head(example_dia_skyline)

+

+}

@@ -12,3 +12,8 @@ data.frame mapping Skyline run names to the corresponding bioreplicates and

 conditions. Used as input to preprocessing function, converting data into

 MSstats format.

 }

+\examples{

+data(example_skyline_annotation)

+head(example_skyline_annotation)

+

+}

@@ -130,3 +130,9 @@ PDF or console plot

 \description{

 General plotting code to produce all QC plots in the application

 }

+\examples{

+data("dia_skyline_model")

+groupComparisonPlots2(dia_skyline_model$ComparisonResult, type="VolcanoPlot",

+                      address=FALSE)

+

+}

@@ -30,9 +30,8 @@ Main function to run MSstatsShiny. All other functions in this package are

 run automatically.

 }

 \examples{

-

-## To run app set launch_app=TRUE

 \dontrun{

+## To run app set launch_app=TRUE

 launch_MSstatsShiny(launch_app=FALSE,testMode=FALSE)

 }

 }

@@ -20,3 +20,14 @@ list of LF modeling results

 \description{

 Main LF function to model MSstatsShiny data.

 }

+\examples{

+data("dia_skyline_summarized")

+comparison <- matrix(c(1, -1, 0, 0, 0, 0, 0, 0, 0, 0),nrow=1)

+row.names(comparison) = "1 vs 128"

+colnames(comparison) = c("1", "128", "16", "2", "256", 

+                         "32", "4", "512", "64", "8")

+model_lf_test = lf_model(dia_skyline_summarized, comparison, 

+                         busy_indicator = FALSE)

+

+

+}

@@ -22,3 +22,32 @@ list of LF Summarization results

 \description{

 Main LF function to calculate MSstatsShiny results.

 }

+\examples{

+data("example_dia_skyline")

+data("example_skyline_annotation")

+testdata = MSstats::SkylinetoMSstatsFormat(example_dia_skyline,

+                                            annotation = example_skyline_annotation,

+                                            filter_with_Qvalue = TRUE, 

+                                            qvalue_cutoff = 0.01, 

+                                            fewMeasurements="remove", 

+                                            removeProtein_with1Feature = TRUE,

+                                            use_log_file = FALSE)

+

+## Source app functionality

+qc_input = list()

+loadpage_input = list()

+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"

+lf_summarization_loop(testdata, qc_input,loadpage_input, busy_indicator=FALSE)

+

+}

@@ -32,3 +32,6 @@ HTML object

 \description{

 Used in UI files to create HTML vizualizations

 }

+\examples{

+radioTooltip("testid", "test_choice", "test_title")

+}

@@ -22,3 +22,44 @@ list of TMT modeling results

 \description{

 Main TMT function to model MSstatsShiny data.

 }

+\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

+qc_input$moderated = FALSE

+

+summarization_tmt_test = tmt_summarization_loop(testdata, qc_input, loadpage_input,

+                                               busy_indicator = FALSE)

+                                               

+comparison=matrix(c(-1,0,0,1),nrow=1)

+row.names(comparison) = "1-0.125"

+colnames(comparison) = c("0.125", "0.5", "0.667", "1")

+

+model_tmt_test = tmt_model(summarization_tmt_test, qc_input, comparison, 

+                           busy_indicator = FALSE)

+

+}

@@ -14,3 +14,8 @@ Data includes one list with two data.tables named \code{ComparisonResult} and

 \code{ModelQC} provides a report on the quality control checks of each protein

 in the dataset.

 }

+\examples{

+data(tmt_pd_model)

+head(tmt_pd_model)

+

+}

@@ -13,3 +13,8 @@ Data includes one list with two data.tables named \code{FeatureLevelData} and

 data. \code{ProteinLevelData} shows the data summarized up to the protein level

 and is used for modeling the data.

 }

+\examples{

+data(tmt_pd_summarized)

+head(tmt_pd_summarized)

+

+}

@@ -22,3 +22,35 @@ 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)

+

+}