Moved CheckInputs_ORA() to HelperChecks.R

saezlab · Nov 5, 2024 · 7c6fcce · 7c6fcce
1 parent 849586e
commit 7c6fcce
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Showing 2 changed files with 139 additions and 137 deletions.
diff --git a/R/HelperChecks.R b/R/HelperChecks.R
@@ -495,3 +495,142 @@ CheckInput_DMA <- function(InputData,
   return(invisible(Settings))
 }
 
+
+################################################################################################
+### ### ### ORA helper function: Internal Function to check function input ### ### ###
+################################################################################################
+
+#' Check input parameters
+#'
+#' @param InputData Passed to main function PreProcessing()
+#' @param SettingsInfo Passed to main function PreProcessing()
+#'
+#' @keywords Input check
+#' @noRd
+#'
+#'
+
+CheckInput_ORA <- function(InputData,
+                           SettingsInfo,
+                           RemoveBackground,
+                           PathwayFile,
+                           PathwayName,
+                           minGSSize,
+                           maxGSSize,
+                           SaveAs_Table,
+                           pCutoff,
+                           PercentageCutoff
+){
+  # 1. The input data:
+  if(class(InputData) != "data.frame"){
+    stop("InputData should be a data.frame. It's currently a ", paste(class(InputData), ".",sep = ""))
+  }
+  if(any(duplicated(row.names(InputData)))==TRUE){
+    stop("Duplicated row.names of InputData, whilst row.names must be unique")
+  }
+
+  # 2. Settings Columns:
+  if(is.vector(SettingsInfo)==FALSE & is.null(SettingsInfo)==FALSE){
+    stop("SettingsInfo should be NULL or a vector. It's currently a ", paste(class(SettingsInfo), ".", sep = ""))
+  }
+
+  if(is.null(SettingsInfo)==FALSE){
+    #"ClusterColumn"
+    if("ClusterColumn" %in% names(SettingsInfo)){
+      if(SettingsInfo[["ClusterColumn"]] %in% colnames(InputData)== FALSE){
+        stop("The ", SettingsInfo[["ClusterColumn"]], " column selected as ClusterColumn in SettingsInfo was not found in InputData. Please check your input.")
+      }
+    }
+
+    #"BackgroundColumn"
+    if("BackgroundColumn" %in% names(SettingsInfo)){
+      if(SettingsInfo[["BackgroundColumn"]] %in% colnames(InputData)== FALSE){
+        stop("The ", SettingsInfo[["BackgroundColumn"]], " column selected as BackgroundColumn in SettingsInfo was not found in InputData. Please check your input.")
+      }
+    }
+
+    #"pvalColumn"
+    if("pvalColumn" %in% names(SettingsInfo)){
+      if(SettingsInfo[["pvalColumn"]] %in% colnames(InputData)== FALSE){
+        stop("The ", SettingsInfo[["pvalColumn"]], " column selected as pvalColumn in SettingsInfo was not found in InputData. Please check your input.")
+      }
+    }
+
+    #"PercentageColumn"
+    if("PercentageColumn" %in% names(SettingsInfo)){
+      if(SettingsInfo[["PercentageColumn"]] %in% colnames(InputData)== FALSE){
+        stop("The ", SettingsInfo[["PercentageColumn"]], " column selected as PercentageColumn in SettingsInfo was not found in InputData. Please check your input.")
+      }
+    }
+
+
+    #"PathwayTerm"
+    if("PathwayTerm" %in% names(SettingsInfo)){
+      if(SettingsInfo[["PathwayTerm"]] %in% colnames(PathwayFile)== FALSE){
+        stop("The ", SettingsInfo[["PathwayTerm"]], " column selected as PathwayTerm in SettingsInfo was not found in PathwayFile. Please check your input.")
+      }else{
+        PathwayFile <- PathwayFile%>%
+          dplyr::rename("term"=SettingsInfo[["PathwayTerm"]])
+        PathwayFile$Description <- PathwayFile$term
+      }
+    }else{
+      stop("SettingsInfo must provide the column name for PathwayTerm in PathwayFile")
+    }
+
+    # PathwayFeature
+    if("PathwayFeature" %in% names(SettingsInfo)){
+      if(SettingsInfo[["PathwayFeature"]] %in% colnames(PathwayFile)== FALSE){
+        stop("The ", SettingsInfo[["PathwayFeature"]], " column selected as PathwayFeature in SettingsInfo was not found in PathwayFile. Please check your input.")
+      }else{
+        PathwayFile <- PathwayFile%>%
+          dplyr::rename("gene"=SettingsInfo[["PathwayFeature"]])
+      }
+    }else{
+      stop("SettingsInfo must provide the column name for PathwayFeature in PathwayFile")
+    }
+
+  }else{
+    stop("you must provide SettingsInfo.")
+  }
+
+  # 3. General Settings
+  if(is.character(PathwayName)==FALSE){
+    stop("Check input. PathwayName must be a character of syntax 'example'.")
+  }
+
+  if(is.logical(RemoveBackground) == FALSE){
+    stop("Check input. RemoveBackground value should be either =TRUE or = FALSE.")
+  }
+
+  if(is.numeric(minGSSize)== FALSE){
+    stop("Check input. The selected minGSSize value should be numeric.")
+  }
+
+  if(is.numeric(maxGSSize)== FALSE){
+    stop("Check input. The selected maxGSSize value should be numeric.")
+  }
+
+  SaveAs_Table_options <- c("txt","csv", "xlsx", "RData")#RData = SummarizedExperiment (?)
+  if(is.null(SaveAs_Table)==FALSE){
+    if((SaveAs_Table %in% SaveAs_Table_options == FALSE)| (is.null(SaveAs_Table)==TRUE)){
+      stop("Check input. The selected SaveAs_Table option is not valid. Please select one of the folowwing: ",paste(SaveAs_Table_options,collapse = ", "),"." )
+    }
+  }
+
+  if(is.null(pCutoff)== FALSE){
+    if(is.numeric(pCutoff)== FALSE | pCutoff > 1 |  pCutoff < 0){
+      stop("Check input. The selected Plot_pCutoff value should be numeric and between 0 and 1.")
+    }
+  }
+
+  if(is.null(PercentageCutoff)== FALSE){
+    if( is.numeric(PercentageCutoff)== FALSE  | PercentageCutoff > 100 | PercentageCutoff < 0){
+      stop("Check input. The selected PercentageCutoff value should be numeric and between 0 and 100.")
+    }
+  }
+
+
+  ## -------- Return Pathways ---------##
+  return(invisible(PathwayFile))
+}
+
diff --git a/R/OverRepresentationAnalysis.R b/R/OverRepresentationAnalysis.R
@@ -301,140 +301,3 @@ StandardORA <- function(InputData,
   }
 
 
-################################################################################################
-### ### ### ORA helper function: Internal Function to check function input ### ### ###
-################################################################################################
-
-#' Check input parameters
-#'
-#' @param InputData Passed to main function PreProcessing()
-#' @param SettingsInfo Passed to main function PreProcessing()
-#'
-#' @keywords Input check
-#' @noRd
-#'
-#'
-
-CheckInput_ORA <- function(InputData,
-                           SettingsInfo,
-                           RemoveBackground,
-                           PathwayFile,
-                           PathwayName,
-                           minGSSize,
-                           maxGSSize,
-                           SaveAs_Table,
-                           pCutoff,
-                           PercentageCutoff
-                           ){
-  # 1. The input data:
-  if(class(InputData) != "data.frame"){
-    stop("InputData should be a data.frame. It's currently a ", paste(class(InputData), ".",sep = ""))
-  }
-  if(any(duplicated(row.names(InputData)))==TRUE){
-    stop("Duplicated row.names of InputData, whilst row.names must be unique")
-  }
-
-  # 2. Settings Columns:
-  if(is.vector(SettingsInfo)==FALSE & is.null(SettingsInfo)==FALSE){
-    stop("SettingsInfo should be NULL or a vector. It's currently a ", paste(class(SettingsInfo), ".", sep = ""))
-  }
-
-  if(is.null(SettingsInfo)==FALSE){
-    #"ClusterColumn"
-    if("ClusterColumn" %in% names(SettingsInfo)){
-      if(SettingsInfo[["ClusterColumn"]] %in% colnames(InputData)== FALSE){
-        stop("The ", SettingsInfo[["ClusterColumn"]], " column selected as ClusterColumn in SettingsInfo was not found in InputData. Please check your input.")
-      }
-    }
-
-    #"BackgroundColumn"
-    if("BackgroundColumn" %in% names(SettingsInfo)){
-      if(SettingsInfo[["BackgroundColumn"]] %in% colnames(InputData)== FALSE){
-        stop("The ", SettingsInfo[["BackgroundColumn"]], " column selected as BackgroundColumn in SettingsInfo was not found in InputData. Please check your input.")
-      }
-    }
-
-    #"pvalColumn"
-    if("pvalColumn" %in% names(SettingsInfo)){
-      if(SettingsInfo[["pvalColumn"]] %in% colnames(InputData)== FALSE){
-        stop("The ", SettingsInfo[["pvalColumn"]], " column selected as pvalColumn in SettingsInfo was not found in InputData. Please check your input.")
-      }
-    }
-
-    #"PercentageColumn"
-    if("PercentageColumn" %in% names(SettingsInfo)){
-      if(SettingsInfo[["PercentageColumn"]] %in% colnames(InputData)== FALSE){
-        stop("The ", SettingsInfo[["PercentageColumn"]], " column selected as PercentageColumn in SettingsInfo was not found in InputData. Please check your input.")
-      }
-    }
-
-
-    #"PathwayTerm"
-    if("PathwayTerm" %in% names(SettingsInfo)){
-      if(SettingsInfo[["PathwayTerm"]] %in% colnames(PathwayFile)== FALSE){
-        stop("The ", SettingsInfo[["PathwayTerm"]], " column selected as PathwayTerm in SettingsInfo was not found in PathwayFile. Please check your input.")
-      }else{
-        PathwayFile <- PathwayFile%>%
-          dplyr::rename("term"=SettingsInfo[["PathwayTerm"]])
-        PathwayFile$Description <- PathwayFile$term
-      }
-    }else{
-      stop("SettingsInfo must provide the column name for PathwayTerm in PathwayFile")
-    }
-
-    # PathwayFeature
-    if("PathwayFeature" %in% names(SettingsInfo)){
-      if(SettingsInfo[["PathwayFeature"]] %in% colnames(PathwayFile)== FALSE){
-        stop("The ", SettingsInfo[["PathwayFeature"]], " column selected as PathwayFeature in SettingsInfo was not found in PathwayFile. Please check your input.")
-      }else{
-        PathwayFile <- PathwayFile%>%
-          dplyr::rename("gene"=SettingsInfo[["PathwayFeature"]])
-      }
-    }else{
-      stop("SettingsInfo must provide the column name for PathwayFeature in PathwayFile")
-    }
-
-  }else{
-    stop("you must provide SettingsInfo.")
-  }
-
-  # 3. General Settings
-  if(is.character(PathwayName)==FALSE){
-    stop("Check input. PathwayName must be a character of syntax 'example'.")
-  }
-
-  if(is.logical(RemoveBackground) == FALSE){
-    stop("Check input. RemoveBackground value should be either =TRUE or = FALSE.")
-  }
-
-  if(is.numeric(minGSSize)== FALSE){
-    stop("Check input. The selected minGSSize value should be numeric.")
-  }
-
-  if(is.numeric(maxGSSize)== FALSE){
-    stop("Check input. The selected maxGSSize value should be numeric.")
-  }
-
-  SaveAs_Table_options <- c("txt","csv", "xlsx", "RData")#RData = SummarizedExperiment (?)
-  if(is.null(SaveAs_Table)==FALSE){
-    if((SaveAs_Table %in% SaveAs_Table_options == FALSE)| (is.null(SaveAs_Table)==TRUE)){
-      stop("Check input. The selected SaveAs_Table option is not valid. Please select one of the folowwing: ",paste(SaveAs_Table_options,collapse = ", "),"." )
-    }
-  }
-
-  if(is.null(pCutoff)== FALSE){
-    if(is.numeric(pCutoff)== FALSE | pCutoff > 1 |  pCutoff < 0){
-    stop("Check input. The selected Plot_pCutoff value should be numeric and between 0 and 1.")
-  }
-  }
-
-  if(is.null(PercentageCutoff)== FALSE){
-    if( is.numeric(PercentageCutoff)== FALSE  | PercentageCutoff > 100 | PercentageCutoff < 0){
-    stop("Check input. The selected PercentageCutoff value should be numeric and between 0 and 100.")
-  }
-  }
-
-
-  ## -------- Return Pathways ---------##
-  return(invisible(PathwayFile))
-}