Add code to body of ensure_numeric_gex() and integrate function into …

…other functions

R/tdm.R

@@ -107,7 +107,10 @@ inv_log_transform = function(data = NULL, file = NULL) {
  data <- fread(file, header=T, data.table=T)
  }
  } 
-
+
+ # ensure gene expression values are numeric
+ data <- ensure_numeric_gex(data)
+
  # Convert the numeric part of the data.table to a matrix.
  # Assuming first column contains gene symbols.
  datamat = data.matrix(data[,2:ncol(data),with=F])
@@ -144,6 +147,9 @@ log_transform_p1 = function(data = NULL, file = NULL) {
  }
  } 
 
+ # ensure gene expression values are numeric
+ data <- ensure_numeric_gex(data)
+
  # Convert the numeric part of the data.table to a matrix.
  # Assuming first column contains gene symbols.
  datamat = data.matrix(data[,2:ncol(data),with=F])
@@ -199,6 +205,10 @@ zero_to_one = function(data) {
 #' 
 #' @export
 zero_to_one_transform = function(datatable) {
+
+ # ensure gene expression values are numeric
+ datatable <- ensure_numeric_gex(datatable)
+
  # Convert the data to a matrix.
  datamat = data.matrix(datatable[,2:ncol(datatable),with=F])
 
@@ -481,6 +491,9 @@ tdm_transform <- function(target_data=NULL,
  # the reference file.
  expression_values <- expression_values[match(genes$gene, expression_values$gene),1:ncol(expression_values),with=FALSE]
 
+ # ensure gene expression values are numeric
+ expression_values <- ensure_numeric_gex(expression_values)
+
  return(expression_values)
 } # end tdm_transform
 
@@ -496,7 +509,21 @@ tdm_transform <- function(target_data=NULL,
 #' @export
 ensure_numeric_gex <- function(input_data) {
 
-
-
- return(something)
-} # ensure_numeric_gex
+ if ("data.table" %in% class(input_data)) {
+
+ gene_names <- as.character(input_data[[1]])
+ gex_values <- t(apply(input_data[,-1], 1, as.numeric))
+
+ return_df <- data.frame(gene_names,
+ gex_values)
+
+ names(return_df) <- names(input_data)
+
+ return(data.table(return_df))
+
+ } else {
+
+ stop("\nInput must be a data.table")
+
+ }
+} # ensure_numeric_gex