@@ -409,8 +409,8 @@ TPP_importCheckConfigTable <- function(infoTable, type = "2D"){

     }

     else if (length(which(!infoTable$RefCol %in% labelColsNew)) != 

              0) {

-      stop("Labels in reference column not found", 

-           " in any of the label columns.")

+      stop(paste("Labels in reference column not found", 

+                 "in any of the label columns."))

     }

     hasCompoundCol <- any(allCols == "Compound")

     if (!hasCompoundCol) {

@@ -669,7 +669,7 @@ filterOutContaminants <- function(dataLong){

           na.rm = TRUE)){

     message("Recomputing ratios!")

     dataOut <- dataLong %>%

-      dplyr::group_by_(idVar, "temperature") %>%

+      group_by(.dots = c(idVar, "temperature")) %>%

       mutate(rel_value = rel_value/rel_value[label == RefCol]) %>%

       ungroup %>%

       filter(!is.na(raw_value)) %>%

@@ -410,7 +410,7 @@ TPP_importCheckConfigTable <- function(infoTable, type = "2D"){

     else if (length(which(!infoTable$RefCol %in% labelColsNew)) != 

              0) {

       stop("Labels in reference column not found", 

-           "in any of teh label columns.")

+           " in any of the label columns.")

     }

     hasCompoundCol <- any(allCols == "Compound")

     if (!hasCompoundCol) {

@@ -627,7 +627,7 @@ annotateDataList <- function(dataList, geneNameVar, configLong,

     conc <- unique_ID <- spread_var <- NULL

   combinedTab <- bind_rows(lapply(dataList, function(dat){

-    datLong <- dat %>% tbl_df() %>%

+    datLong <- dat %>% as_tibble() %>%

       gather(channel, signal, matches(intensityStr), matches(fcStr)) %>%

       mutate(label = gsub(fcStr, "", gsub(intensityStr, "", channel))) %>%

       left_join(configLong %>% 

@@ -741,8 +741,8 @@ filterOutContaminants <- function(dataLong){

 renameColumns <- function(dataLong, idVar, geneNameVar){

   clustername <- representative <- NULL

-  dplyr::rename_(dataLong, "representative" = idVar, 

-                 "clustername" = geneNameVar) %>%

+  dplyr::rename(dataLong, "representative" = idVar, 

+                "clustername" = geneNameVar) %>%

     group_by(clustername) %>%

     mutate(representative =

              .paste_rmNA(unique(unlist(strsplit(representative, 

@@ -66,13 +66,14 @@

   return(data)

 }

+#' @import dplyr

 .TPP_importFct_removeDuplicates <- function(inDF, refColName, 

                                            nonNAColNames, qualColName){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   message("Removing duplicate identifiers using quality column '", 

           qualColName, "'...")

-  nonUniques <- unique(inDF[duplicated(inDF[[refColName]]), 

+  nonUniques <- unique(as_tibble(inDF)[duplicated(inDF[[refColName]]), 

                            refColName])

   retDF <- subset(inDF, !(get(refColName) %in% nonUniques))

   if(nrow(nonUniques)){

@@ -1,4 +1,4 @@

-TPP_importFct_CheckDataFormat <- function (files, dataframes, expNames){

+.TPP_importFct_CheckDataFormat <- function (files, dataframes, expNames){

     # internal function copied from TPP package to avoid 

     # import of non-exported package functions

     . <- NULL

@@ -47,7 +47,7 @@ TPP_importFct_CheckDataFormat <- function (files, dataframes, expNames){

 #' @importFrom utils read.delim

 #' @importFrom RCurl url.exists

-TPP_importFct_readFiles <- function (files, naStrs){

+.TPP_importFct_readFiles <- function (files, naStrs){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   expNames <- names(files)

@@ -66,51 +66,53 @@ TPP_importFct_readFiles <- function (files, naStrs){

   return(data)

 }

-TPP_importFct_removeDuplicates <- function(inDF, refColName, 

+.TPP_importFct_removeDuplicates <- function(inDF, refColName, 

                                            nonNAColNames, qualColName){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   message("Removing duplicate identifiers using quality column '", 

           qualColName, "'...")

-  nonUniques = unique(inDF[duplicated(inDF[[refColName]]), 

+  nonUniques <- unique(inDF[duplicated(inDF[[refColName]]), 

                            refColName])

-  retDF = subset(inDF, !(get(refColName) %in% nonUniques))

-  for (nU in nonUniques) {

-    tmpDF = subset(inDF, get(refColName) == nU)

-    nonNArows = NULL

-    for (r in seq_len(nrow(tmpDF))) {

-      if (any(!is.na(tmpDF[r, nonNAColNames]))) {

-        nonNArows = c(nonNArows, r)

-      }

-    }

-    if (length(nonNArows) > 1) {

-      if (is.null(qualColName)) {

-        useRow = 1

-      }

-      else {

-        qualVals = tmpDF[nonNArows, qualColName]

-        useRow = match(max(qualVals), qualVals)

+  retDF <- subset(inDF, !(get(refColName) %in% nonUniques))

+  if(nrow(nonUniques)){

+      for (nU in nonUniques) {

+          tmpDF <- subset(inDF, get(refColName) == nU)

+          nonNArows <- NULL

+          for (r in seq_len(nrow(tmpDF))) {

+              if (any(!is.na(tmpDF[r, nonNAColNames]))) {

+                  nonNArows <- c(nonNArows, r)

+              }

+          }

+          if (length(nonNArows) > 1) {

+              if (is.null(qualColName)) {

+                  useRow <- 1

+              }

+              else {

+                  qualVals <- tmpDF[nonNArows, qualColName]

+                  useRow <- match(max(qualVals), qualVals)

+              }

+          }

+          else {

+              useRow <- nonNArows[1]

+          }

+          retDF <- rbind(retDF, tmpDF[useRow, ])

       }

-    }

-    else {

-      useRow = nonNArows[1]

-    }

-    retDF = rbind(retDF, tmpDF[useRow, ])

   }

   message(nrow(retDF), " out of ", nrow(inDF), 

           " rows kept for further analysis.")

   return(retDF)

 }

-TPP_replaceZeros <- function(x){

+.TPP_replaceZeros <- function(x){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   x[which(x == 0)] <- NA

   return(x)

 }

-TPP_importFct_rmZeroSias <- function(configTable, data.list, 

-                                     intensityStr){

+.TPP_importFct_rmZeroSias <- function(data.list, 

+                                      intensityStr){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   out <- lapply(names(data.list), function(l.name) {

@@ -119,7 +121,7 @@ TPP_importFct_rmZeroSias <- function(configTable, data.list,

     intensity.cols <- grep(intensityStr, colsTmp, value = TRUE)

     intensity.df <- subset(datTmp, select = intensity.cols) %>% 

       mutate_all(as.character) %>% mutate_all(as.numeric)

-    new.intensity.df <- intensity.df %>% mutate_all(TPP_replaceZeros)

+    new.intensity.df <- intensity.df %>% mutate_all(.TPP_replaceZeros)

     datTmp[, intensity.cols] <- new.intensity.df

     return(datTmp)

   })

@@ -127,7 +129,7 @@ TPP_importFct_rmZeroSias <- function(configTable, data.list,

   return(out)

 }

-TPP_importFct_checkExperimentCol <- function(expCol){

+.TPP_importFct_checkExperimentCol <- function(expCol){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   if (is.null(expCol)) {

@@ -149,7 +151,7 @@ TPP_importFct_checkExperimentCol <- function(expCol){

   return(newExpNames)

 }

-TPP_importFct_checkComparisons <- function(confgTable){

+.TPP_importFct_checkComparisons <- function(confgTable){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   expConds <- confgTable$Condition

@@ -167,7 +169,7 @@ TPP_importFct_checkComparisons <- function(confgTable){

   }

   validCompCols <- compCols[!comp_unequal_two]

   allCompStrs <- c()

-  if (length(validCompCols) > 0) {

+  if (length(validCompCols)) {

     message("Comparisons will be performed between the following experiments:")

     for (colName in validCompCols) {

       current_compEntries <- confgTable[[colName]]

@@ -196,7 +198,7 @@ TPP_importFct_checkComparisons <- function(confgTable){

 }

 #' @importFrom stringr str_to_title

-TPP_importFct_checkConditions <- function(condInfo, 

+.TPP_importFct_checkConditions <- function(condInfo, 

                                           expectedLength){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

@@ -227,7 +229,7 @@ TPP_importFct_checkConditions <- function(condInfo,

   return(condInfo)

 }

-TPP_checkFunctionArgs <- 

+.TPP_checkFunctionArgs <- 

   function(functionCall, expectedArguments){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

@@ -242,7 +244,7 @@ TPP_checkFunctionArgs <-

   })

 }

-TPP_nonLabelColumns <- function(){

+.TPP_nonLabelColumns <- function(){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   out <- data.frame(

@@ -259,12 +261,12 @@ TPP_nonLabelColumns <- function(){

   return(out)

 }

-TPP_detectLabelColumnsInConfigTable <- 

+.TPP_detectLabelColumnsInConfigTable <- 

   function(allColumns){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

-  TPP_checkFunctionArgs(match.call(), c("allColumns"))

-  noLabelCols <- TPP_nonLabelColumns()$column %>% 

+  .TPP_checkFunctionArgs(match.call(), c("allColumns"))

+  noLabelCols <- .TPP_nonLabelColumns()$column %>% 

     as.character %>% 

     unique

   compCols <- grep("comparison", allColumns, value = TRUE, 

@@ -274,7 +276,7 @@ TPP_detectLabelColumnsInConfigTable <-

   return(labelCols)

 }

-TPP_importCheckTemperatures <- function(temp){

+.TPP_importCheckTemperatures <- function(temp){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   tempMatrix <- as.matrix(temp)

@@ -290,7 +292,7 @@ TPP_importCheckTemperatures <- function(temp){

 #' @importFrom openxlsx read.xlsx

 #' @importFrom utils read.table

-TPP_importFct_readConfigTable <- function(cfg){

+.TPP_importFct_readConfigTable <- function(cfg){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   if (is.character(cfg)) {

@@ -326,11 +328,23 @@ TPP_importFct_readConfigTable <- function(cfg){

   return(cfg)

 }

-TPP_importCheckConfigTable <- function (infoTable, type = "2D"){

-  # internal function copied from TPP package to avoid 

-  # import of non-exported package functions

-  TPP_checkFunctionArgs(match.call(), c("infoTable", "type"))

-  Experiment = Path = Compound <- NULL

+#' Import and chech configuration table

+#' 

+#' @param infoTable character string of a file path to

+#' a config table (excel,txt or csv file) or data frame

+#' containing a config table

+#' @param type charater string indicating dataset type

+#' default is 2D

+#' 

+#' @return data frame with config table

+#' 

+#' @examples 

+#' data("config_tab")

+#' TPP_importCheckConfigTable(config_tab, type = "2D")

+#' @export

+TPP_importCheckConfigTable <- function(infoTable, type = "2D"){

+  .TPP_checkFunctionArgs(match.call(), c("infoTable", "type"))

+  Experiment <- Path <- Compound <- NULL

   isValidDF <- FALSE

   if (is.data.frame(infoTable)) {

     if ((ncol(infoTable) > 1) & 

@@ -349,9 +363,9 @@ TPP_importCheckConfigTable <- function (infoTable, type = "2D"){

   if (!isValidType) {

     stop("'type' must have this value: '2D'")

   }

-  infoTable <- TPP_importFct_readConfigTable(cfg = infoTable)

+  infoTable <- .TPP_importFct_readConfigTable(cfg = infoTable)

   infoTable$Experiment <- 

-    TPP_importFct_checkExperimentCol(infoTable$Experiment)

+    .TPP_importFct_checkExperimentCol(infoTable$Experiment)

   infoTable <- subset(infoTable, Experiment != "")

   givenPaths <- NULL

   if (any("Path" %in% colnames(infoTable))) {

@@ -366,7 +380,7 @@ TPP_importCheckConfigTable <- function (infoTable, type = "2D"){

   compStrs <- NA

   infoTable$Condition <- NULL

   allCols <- colnames(infoTable)

-  labelCols <- TPP_detectLabelColumnsInConfigTable(allColumns = allCols)

+  labelCols <- .TPP_detectLabelColumnsInConfigTable(allColumns = allCols)

   labelValues <- infoTable[, labelCols]

   labelValuesNum <- suppressWarnings(labelValues %>% apply(2, 

                                                            as.numeric))

@@ -412,7 +426,7 @@ TPP_importCheckConfigTable <- function (infoTable, type = "2D"){

   }

   else {

     temperatures <- subset(infoTable, select = labelColsNew)

-    tempMatrix <- TPP_importCheckTemperatures(temp = temperatures)

+    tempMatrix <- .TPP_importCheckTemperatures(temp = temperatures)

     infoList <- list(

       expNames = as.character(infoTable$Experiment), 

       expCond = infoTable$Condition, files = givenPaths, 

@@ -423,6 +437,45 @@ TPP_importCheckConfigTable <- function (infoTable, type = "2D"){

   return(out)

 }

+#' Import 2D-TPP dataset main function

+#' 

+#' @param configTable character string of a file path to a config table

+#' @param data possible list of datasets from different MS runs 

+#' corresponding to a 2D-TPP dataset, circumvents loading datasets 

+#' referencend in config table, default is NULL

+#' @param idVar character string indicating which data column provides the 

+#' unique identifiers for each protein.

+#' @param intensityStr character string indicating which columns contain 

+#' raw intensities measurements

+#' @param fcStr character string indicating which columns contain the actual 

+#' fold change values. Those column names containing the suffix \code{fcStr} 

+#' will be regarded as containing fold change values.

+#' @param naStrs character vector indicating missing values in the data table. 

+#' When reading data from file, this value will be passed on to the argument 

+#' \code{na.strings} in function \code{read.delim}.

+#' @param addCol character string indicating additional column to import

+#' @param nonZeroCols column like default qssm that should be imported and

+#' requested to be non-zero in analyzed data

+#' @param qualColName character string indicating which column can be used for 

+#' additional quality criteria when deciding between different non-unique 

+#' protein identifiers.

+#' 

+#' @return list of data frames containing different

+#' datasets

+#' 

+#' @examples 

+#' data("config_tab")

+#' data("raw_dat_list")

+#' dataList <- import2dMain(configTable = config_tab,

+#'                          data = raw_dat_list,

+#'                          idVar = "protein_id",

+#'                          fcStr = "rel_fc_",

+#'                          addCol = "gene_name",

+#'                          naStrs = NA,

+#'                          intensityStr = "signal_sum_",

+#'                          nonZeroCols = "qusm",

+#'                          qualColName = "qupm")

+#' @export

 import2dMain <- function(configTable, data, idVar, fcStr,

                          addCol, naStrs, intensityStr,

                          qualColName, nonZeroCols){

@@ -434,20 +487,18 @@ import2dMain <- function(configTable, data, idVar, fcStr,

       files <- NULL

     }

   }

-  Experiment = Compound = Temperature = RefCol <- NULL

+  Experiment <- Compound <- Temperature <- RefCol <- NULL

   expNames <- configTable$Experiment

-  argList <- TPP_importFct_CheckDataFormat(dataframes = data, 

+  argList <- .TPP_importFct_CheckDataFormat(dataframes = data, 

                                            files = files,

                                            expNames = expNames)

   data <- argList[["dataframes"]]

   files <- argList[["files"]]

   if (!is.null(files)) {

     files2 <- files[!duplicated(names(files))]

-    data <- TPP_importFct_readFiles(files = files2, 

+    data <- .TPP_importFct_readFiles(files = files2, 

                                     naStrs = naStrs)

   }

-  configTable %>% group_by(Experiment, Compound,

-                           Temperature, RefCol)

   iVec <- seq_len(nrow(configTable))

   dataList <- lapply(iVec, function(iTmp) {

     rowTmp <- configTable[iTmp, ]

@@ -459,7 +510,7 @@ import2dMain <- function(configTable, data, idVar, fcStr,

                   "RefCol", "Path", "Condition")

     allCols <- colnames(rowTmp)

     labelCols <- setdiff(allCols, noFCCols)

-    labelValues <- suppressMessages(rowTmp[, labelCols] %>%

+    labelValues <- suppressWarnings(rowTmp[, labelCols] %>%

                                       as.numeric)

     labelColsNum <- labelCols[!is.na(labelValues)]

     signalCols <- paste(intensityStr, labelColsNum, sep = "")

@@ -480,7 +531,7 @@ import2dMain <- function(configTable, data, idVar, fcStr,

            notFound, paste("'. Please check the suffices and the", 

                            "additional column names you have specified."))

     }

-    dataFiltered <- TPP_importFct_removeDuplicates(

+    dataFiltered <- .TPP_importFct_removeDuplicates(

       inDF = dataTmp,refColName = idVar, 

       nonNAColNames = dataCols, 

       qualColName = qualColName[1])

@@ -498,17 +549,24 @@ import2dMain <- function(configTable, data, idVar, fcStr,

     return(newName)

   }, "")

   names(dataList) <- newNames

-  out <- TPP_importFct_rmZeroSias(configTable = configTable, 

-                                  data.list = dataList,

-                                  intensityStr = intensityStr)

+  out <- .TPP_importFct_rmZeroSias(data.list = dataList,

+                                   intensityStr = intensityStr)

   return(out)

 }

+#' Tranform configuration table from wide to long

+#' 

+#' @param configWide data frame containing a config table

+#' @return data frame containing config table in long format 

+#' 

 #' @importFrom tidyr gather

+#' @examples 

+#' data("config_tab")

+#' configWide2Long(configWide = config_tab)

+#' 

+#' @export

 configWide2Long <- function(configWide){

-  # internal function to tranform config table into long format

-  

-  Path <- label <- conc <- Compound <- Experiment <- 

+ Path <- label <- conc <- Compound <- Experiment <- 

     Temperature <- RefCol <- NULL

   if(any(grepl("Path", colnames(configWide)))){

@@ -525,11 +583,45 @@ configWide2Long <- function(configWide){

   }

 }

+#' Annotate imported data list using a config table

+#' @param dataList list of datasets from different MS runs 

+#' corresponding to a 2D-TPP dataset

+#' @param geneNameVar character string of the column name that describes

+#' the gene name of a given protein in the raw data files

+#' @param configLong long formatted data frame of a corresponding

+#' config table

+#' @param intensityStr character string indicating which columns contain 

+#' raw intensities measurements

+#' @param fcStr character string indicating which columns contain the actual 

+#' fold change values. Those column names containing the suffix \code{fcStr} 

+#' will be regarded as containing fold change values.

+#' 

+#' @return data frame containing all data annotated

+#' by information supplied in the config table

+#'   

 #' @importFrom tidyr spread

+#' 

+#' @examples 

+#' data("config_tab")

+#' data("raw_dat_list")

+#' dataList <- import2dMain(configTable = config_tab,

+#'                          data = raw_dat_list,

+#'                          idVar = "protein_id",

+#'                          fcStr = "rel_fc_",

+#'                          addCol = "gene_name",

+#'                          naStrs = NA,

+#'                          intensityStr = "signal_sum_",

+#'                          nonZeroCols = "qusm",

+#'                          qualColName = "qupm")

+#' configLong <- configWide2Long(configWide = config_tab)

+#' annotateDataList(dataList = dataList,

+#'                  geneNameVar = "gene_name",

+#'                  configLong = configLong,

+#'                  intensityStr = "signal_sum_",

+#'                  fcStr = "rel_fc_")

+#' @export

 annotateDataList <- function(dataList, geneNameVar, configLong,

                              intensityStr, fcStr){

-  # internal function to annotate list of 2D-TPP data subtables with

-  # information from config table

   channel <- signal <- Temperature <- RefCol <- label <- 

     conc <- unique_ID <- spread_var <- NULL

@@ -548,13 +640,25 @@ annotateDataList <- function(dataList, geneNameVar, configLong,

   return(combinedTab)

 }

+#' Filter out contaminants

+#' 

+#' @param dataLong long format data frame of imported dataset

+#' 

+#' @return data frame containing full dataset filtered to 

+#' contain no contaminants

+#' 

+#' @examples 

+#' data("simulated_cell_extract_df")

+#' filterOutContaminants(simulated_cell_extract_df)

+#' 

+#' @export

 filterOutContaminants <- function(dataLong){

   # internal function to filter out contaminants

   representative <- NULL

   filter(dataLong, !grepl("##", representative))

 }

-checkRatioRef <- function(dataLong, idVar, concFactor = 1e6){

+.checkRatioRef <- function(dataLong, idVar, concFactor = 1e6){

   # internal function to check that protein 

   # fold changes are computed

   # relative to the correct TMT channel

@@ -583,7 +687,7 @@ checkRatioRef <- function(dataLong, idVar, concFactor = 1e6){

 }

 #' @importFrom stats median

-medianNormalizeRatios <- function(dataLong){

+.medianNormalizeRatios <- function(dataLong){

   # internal function to perform median normalization 

   # of ratios

   rel_value <- temperature <- conc <- 

@@ -599,17 +703,48 @@ medianNormalizeRatios <- function(dataLong){

   return(dataOut)

 }

+#' Rename columns of imported data frame

+#' 

+#' @param dataLong long format data frame of imported dataset

+#' @param idVar character string indicating which data column provides the 

+#' unique identifiers for each protein.

+#' @param geneNameVar character string of the column name that describes

+#' the gene name of a given protein in the raw data files

+#' 

+#' @return data frame containing imported data with renamed

+#' columns

+#' 

+#' @examples 

+#' data("config_tab")

+#' data("raw_dat_list")

+#' 

+#' dataList <- import2dMain(configTable = config_tab,

+#'                          data = raw_dat_list,

+#'                          idVar = "protein_id",

+#'                          fcStr = "rel_fc_",

+#'                          addCol = "gene_name",

+#'                          naStrs = NA,

+#'                          intensityStr = "signal_sum_",

+#'                          nonZeroCols = "qusm",

+#'                          qualColName = "qupm")

+#' configLong <- configWide2Long(configWide = config_tab)

+#' annoDat <- annotateDataList(dataList = dataList,

+#'                             geneNameVar = "gene_name",

+#'                             configLong = configLong,

+#'                             intensityStr = "signal_sum_",

+#'                             fcStr = "rel_fc_")

+#' renameColumns(annoDat, 

+#'               idVar = "protein_id", 

+#'               geneNameVar = "gene_name")

+#' @export

 renameColumns <- function(dataLong, idVar, geneNameVar){

-  # internal function to rename column names to 

-  # match lazyeval variable

-  # names of main function

   clustername <- representative <- NULL

   dplyr::rename_(dataLong, "representative" = idVar, 

                  "clustername" = geneNameVar) %>%

     group_by(clustername) %>%

     mutate(representative =

-             paste_rmNA(unique(unlist(strsplit(representative, 

+             .paste_rmNA(unique(unlist(strsplit(representative, 

                                                split = "\\|"))), 

                         sep = "|")) %>%

     ungroup()

@@ -698,12 +833,12 @@ import2dDataset <- function(configTable, data,

                                intensityStr = intensityStr,

                                fcStr = fcStr)

-  dataRatioChecked <- checkRatioRef(dataLong, idVar = idVar,

-                                    concFactor = concFactor)

+  dataRatioChecked <- .checkRatioRef(dataLong, idVar = idVar,

+                                     concFactor = concFactor)

   if(medianNormalizeFC){

     message("Median normalizing fold changes...")

-    dataNorm <- medianNormalizeRatios(dataRatioChecked)

+    dataNorm <- .medianNormalizeRatios(dataRatioChecked)

   }else{

     dataNorm <- dataRatioChecked

   }

@@ -1,46 +1,48 @@

 TPP_importFct_CheckDataFormat <- function (files, dataframes, expNames){

-  # internal function copied from TPP package to avoid 

-  # import of non-exported package functions

-  . <- NULL

-  isDF <- !is.null(dataframes)

-  isF <- !is.null(files)

-  isBoth <- isDF & isF

-  isNone <- !(isDF | isF)

-  if (isBoth) {

-    stop("Data import function received a filename AND a dataframe object. \n

-         Please specify only one.")

-  }

-  else if (isNone) {

-    stop("Data import function requires a filename or a dataframe object. \n

-         Please specify one.")

-  }

-  if (isDF) {

-    isClassList <- is.list(dataframes) && !is.data.frame(dataframes)

-    isClassDF <- is.data.frame(dataframes)

-    if (isClassList) {

-      classesInList <- dataframes %>% 

-        vapply(. %>% inherits(., "data.frame"), TRUE)

-      if (!all(classesInList)) {

-        stop(paste("Argument 'dataframes' contains elements that are", 

-                   "not of type 'data.frame' at the following positions: "), 

-             which(!classesInList) %>% paste(collapse = ", "), 

-             ".")

-      }

+    # internal function copied from TPP package to avoid 

+    # import of non-exported package functions

+    . <- NULL

+    isDF <- !is.null(dataframes)

+    isF <- !is.null(files)

+    isBoth <- isDF & isF

+    isNone <- !(isDF | isF)

+    if (isBoth) {

+        stop("Data import function received a",

+             " filename AND a dataframe object. \n",

+             "Please specify only one.")

     }

-    else if (isClassDF) {

-      dataframes <- list(dataframes)

-      names(dataframes) <- expNames

+    else if (isNone) {

+        stop("Data import function requires a", 

+             " filename or a dataframe object. \n",

+             "Please specify one.")

     }

-    else {

-      stop("Argument 'dataframes' must be either an object of class \n

-           'data.frame', or a list of such objects.")

+    if (isDF) {

+        isClassList <- is.list(dataframes) && !is.data.frame(dataframes)

+        isClassDF <- is.data.frame(dataframes)

+        if (isClassList) {

+            classesInList <- dataframes %>% 

+            vapply(. %>% inherits(., "data.frame"), TRUE)

+            if (!all(classesInList)) {

+                stop(paste("Argument 'dataframes' contains", 

+                           "elements that are not of type", 

+                           "'data.frame' at the following positions: "), 

+                     which(!classesInList) %>% paste(collapse = ", "), ".")

+            }

+          }

+          else if (isClassDF) {

+              dataframes <- list(dataframes)

+              names(dataframes) <- expNames

+          }

+          else {

+              stop("Argument 'dataframes' must be either an object of class \n

+                   'data.frame', or a list of such objects.")

+          }

     }

-  }

-  if (isF) {

-    files <- as.character(files)

-    names(files) <- expNames

-  }

-  return(list(files = files, dataframes = dataframes))

+    if (isF) {

+        files <- as.character(files)

+        names(files) <- expNames

+    }

+    return(list(files = files, dataframes = dataframes))

 }

 #' @importFrom utils read.delim

@@ -95,7 +97,8 @@ TPP_importFct_removeDuplicates <- function(inDF, refColName,

     }

     retDF = rbind(retDF, tmpDF[useRow, ])

   }

-  message(nrow(retDF), " out of ", nrow(inDF), " rows kept for further analysis.")

+  message(nrow(retDF), " out of ", nrow(inDF), 

+          " rows kept for further analysis.")

   return(retDF)

 }

@@ -128,14 +131,16 @@ TPP_importFct_checkExperimentCol <- function(expCol){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   if (is.null(expCol)) {

-    m <- "Config table needs an 'Experiment' column with unique experiment IDs."

+    m <- paste("Config table needs an 'Experiment'", 

+               "column with unique experiment IDs.")

     stop(m, "\n")

   }

   oldExpNames <- expCol

   newExpNames <- gsub("([^[:alnum:]])", "_", expCol)

   iChanged <- oldExpNames != newExpNames

   if (any(iChanged)) {

-    m1 <- "Replaced non-alphanumeric characters in the 'Experiment' column entries:"

+    m1 <- paste("Replaced non-alphanumeric characters", 

+                "in the 'Experiment' column entries:")

     m2 <- paste("'", paste(oldExpNames[iChanged], collapse = "', '"), 

                 "'\nby\n'", paste(newExpNames[iChanged], collapse = "', '"), 

                 sep = "")

@@ -197,32 +202,42 @@ TPP_importFct_checkConditions <- function(condInfo,

   # import of non-exported package functions

   flagGenerateConds <- FALSE

   if (is.null(condInfo)) {

-    message("No information about experimental conditions given. Assigning NA instead.\n

-            Reminder: recognition of Vehicle and Treatment groups during pairwise \n

-            comparisons is only possible when they are specified in the config table.\n")

+    message("No information about experimental conditions given.", 

+            "Assigning NA instead.\n",

+            "Reminder: recognition of Vehicle and Treatment groups", 

+            "during pairwise \n",

+            "comparisons is only possible when they are specified ",

+            "in the config table.\n")

     condInfo <- rep(NA_character_, expectedLength)

   }

   else {

-    condInfo <- as.character(condInfo) %>% stringr::str_to_title()

+    condInfo <- as.character(condInfo) %>% 

+      stringr::str_to_title()

     condLevels <- unique(condInfo)

-    invalidLevels = setdiff(condLevels, c("Treatment", "Vehicle"))

+    invalidLevels = 

+      setdiff(condLevels, c("Treatment", "Vehicle"))

     if (length(invalidLevels) > 0) {

       stop("The entry '", invalidLevels, 

-           paste("' in the condition column is invalid. Only the values 'Treatment' and", 

-                 "'Vehicle' are allowed. Please correct this and start again."))

+           paste("' in the condition column is invalid.", 

+                 "Only the values 'Treatment' and", 

+                 "'Vehicle' are allowed. Please correct", 

+                 "this and start again."))

     }

   }

   return(condInfo)

 }

-TPP_checkFunctionArgs <- function(functionCall, expectedArguments){

+TPP_checkFunctionArgs <- 

+  function(functionCall, expectedArguments){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   myArgs <- names(functionCall)

   lapply(expectedArguments, function(arg) {

     if (!arg %in% myArgs) {

-      stop("Error in ", paste(functionCall)[1], ": argument '", 

-           arg, "' is missing, with no default", call. = FALSE)

+      stop("Error in ", paste(functionCall)[1], 

+           ": argument '", 

+           arg, "' is missing, with no default", 

+           call. = FALSE)

     }

   })

 }

@@ -244,11 +259,13 @@ TPP_nonLabelColumns <- function(){

   return(out)

 }

-TPP_detectLabelColumnsInConfigTable <- function(allColumns){

+TPP_detectLabelColumnsInConfigTable <- 

+  function(allColumns){

   # internal function copied from TPP package to avoid 

   # import of non-exported package functions

   TPP_checkFunctionArgs(match.call(), c("allColumns"))

-  noLabelCols <- TPP_nonLabelColumns()$column %>% as.character %>% 

+  noLabelCols <- TPP_nonLabelColumns()$column %>% 

+    as.character %>% 

     unique

   compCols <- grep("comparison", allColumns, value = TRUE, 

                    ignore.case = TRUE)

@@ -265,7 +282,8 @@ TPP_importCheckTemperatures <- function(temp){

   naRows <- apply(is.na(tempMatrix), 1, all)

   if (any(naRows)) {

     stop("Row(s) ", paste(which(naRows), collapse = ", "), 

-         " in the configuration table contain only missing temperature values.")

+         " in the configuration table contain", 

+         " only missing temperature values.")

   }

   return(tempMatrix)

 }

@@ -280,24 +298,28 @@ TPP_importFct_readConfigTable <- function(cfg){

       strChunks <- strsplit(cfg, "\\.")[[1]]

       fileExtension <- strChunks[length(strChunks)]

       if (fileExtension == "txt") {

-        tab <- read.table(file = cfg, header = TRUE, 

-                          check.names = FALSE, stringsAsFactors = FALSE, 

-                          sep = "\t")

+        tab <- read.table(

+          file = cfg, header = TRUE, 

+          check.names = FALSE, stringsAsFactors = FALSE, 

+          sep = "\t")

       }

       else if (fileExtension == "csv") {

-        tab <- read.table(file = cfg, header = TRUE, 

-                          check.names = FALSE, stringsAsFactors = FALSE, 

-                          sep = ",")

+        tab <- read.table(

+          file = cfg, header = TRUE, 

+          check.names = FALSE, stringsAsFactors = FALSE, 

+          sep = ",")

       }

       else if (fileExtension == "xlsx") {

         tab <- openxlsx::read.xlsx(cfg)

       }

       else {

-        stop("Error during data import: ", cfg, " does not belong to a valid configuration file.")

+        stop("Error during data import: ", cfg, 

+             " does not belong to a valid configuration file.")

       }

     }

     else {

-      stop("Error during data import: ", cfg, " does not belong to a valid configuration file.")

+      stop("Error during data import: ", cfg, 

+           " does not belong to a valid configuration file.")

     }

     cfg <- tab

   }

@@ -311,21 +333,25 @@ TPP_importCheckConfigTable <- function (infoTable, type = "2D"){

   Experiment = Path = Compound <- NULL

   isValidDF <- FALSE

   if (is.data.frame(infoTable)) {

-    if ((ncol(infoTable) > 1) & ("Experiment" %in% colnames(infoTable))) {

+    if ((ncol(infoTable) > 1) & 

+        ("Experiment" %in% colnames(infoTable))) {

       isValidDF <- TRUE

     }

   }

   if (!is.character(infoTable) & !isValidDF) {

-    stop("'infoTable' must either be a data frame with an 'Experiment' column \n

-         and at least one isobaric label column, or a filename pointing at a \n

-         table that fulfills the same criteria")

+    stop("'infoTable' must either be a data frame", 

+         " with an 'Experiment' column \n",

+         "and at least one isobaric label column,", 

+         "or a filename pointing at a \n",

+         "table that fulfills the same criteria")

   }

   isValidType <- type %in% c("2D")

   if (!isValidType) {

     stop("'type' must have this value: '2D'")

   }

   infoTable <- TPP_importFct_readConfigTable(cfg = infoTable)

-  infoTable$Experiment <- TPP_importFct_checkExperimentCol(infoTable$Experiment)

+  infoTable$Experiment <- 

+    TPP_importFct_checkExperimentCol(infoTable$Experiment)

   infoTable <- subset(infoTable, Experiment != "")

   givenPaths <- NULL

   if (any("Path" %in% colnames(infoTable))) {

@@ -360,31 +386,38 @@ TPP_importCheckConfigTable <- function (infoTable, type = "2D"){

   if (type == "2D") {

     temperatures <- infoTable$Temperature

     if (is.null(temperatures) | length(temperatures) < 2) {

-      m1 <- "Insufficient temperatures (<2) specified in config file."

-      m2 <- "Does your configuration table have the correct column names?"

+      m1 <- paste("Insufficient temperatures (<2)", 

+                  "specified in config file.")

+      m2 <- paste("Does your configuration table", 

+                  "have the correct column names?")

       stop(m1, "\n", m2)

     }

     else if (length(which(!infoTable$RefCol %in% labelColsNew)) != 

              0) {

-      stop("Labels in reference column not found in any of teh label columns.")

+      stop("Labels in reference column not found", 

+           "in any of teh label columns.")

     }

     hasCompoundCol <- any(allCols == "Compound")

     if (!hasCompoundCol) {

-      m <- "Config table of a 2D-TPP experiment needs a 'Compound' column."

+      m <- paste("Config table of a 2D-TPP experiment", 

+                 "needs a 'Compound' column.")

       stop(m, "\n")

     }

     else {

-      infoTable <- infoTable %>% mutate(Compound = gsub("([^[:alnum:]])", 

-                                                        "_", Compound))

+      infoTable <- infoTable %>% 

+        mutate(Compound = 

+                 gsub("([^[:alnum:]])", "_", Compound))

     }

     out <- infoTable