@sjcrh/proteinpaint-server 2.78.0 → 2.79.1-0

package/utils/regression.R

@@ -109,7 +109,7 @@ benchmark[["prepareDataTable"]] <- unbox(paste(round(as.numeric(dtime), 4), attr
 ##################
 
 stime <- Sys.time()
-formulas <- buildFormulas(input$outcome, input$independent, input$neuroOnc)
+formulas <- buildFormulas(input$outcome, input$independent, input$includeUnivariate)
 etime <- Sys.time()
 dtime <- etime - stime
 benchmark[["buildFormulas"]] <- unbox(paste(round(as.numeric(dtime), 4), attr(dtime, "units")))
@@ -137,9 +137,9 @@ benchmark[["runRegression"]] <- unbox(paste(round(as.numeric(dtime), 4), attr(dt
 # PARSE RESULTS #
 ##################
 
-if (isTRUE(input$neuroOnc) && nrow(input$independent) > 1) {
-  # neuro-oncology dataset using multiple covariates
-  # parse the results from univariate and multivariate analyses
+if (isTRUE(input$includeUnivariate)) {
+  # univariate analysis included along with multivariate analysis
+  # parse the results
   # TODO: this function will not work with snplocus regression because it
   # will combine results from multiple analyses into a single set of results
   reg_results <- parseUniMultiResults(reg_results, input$regressionType)

package/utils/regression.utils.R

@@ -54,7 +54,7 @@ cubic_spline <- function(values, knots) {
 }
 
 # build formulas
-buildFormulas <- function(outcome, independent, neuroOnc) {
+buildFormulas <- function(outcome, independent, includeUnivariate) {
   # first, format variables for building formulas
   
   # declare new objects
@@ -117,8 +117,6 @@ buildFormulas <- function(outcome, independent, neuroOnc) {
     }
   }
   
-  if (isTRUE(neuroOnc) && length(formula_interaction) > 0) stop ("interactions not supported in neuro-onc datasets")
-  
   # combine variables into formula(s)
   # if snplocus snps are present, then prepare a
   # separate formula for each snplocus snp
@@ -152,9 +150,10 @@ buildFormulas <- function(outcome, independent, neuroOnc) {
     }
   } else {
     # no snplocus snps
-    if (isTRUE(neuroOnc) && length(formula_independent) > 1) {
-      # neuro-onc dataset using multiple covariates
-      # build multivariate and univariate formulas
+    if (isTRUE(includeUnivariate)) {
+      # include univariate formulas along with the multivariate formula
+      if (length(formula_independent) < 2) stop("must have multiple covariates to build multivariate and univariate formulas")
+      if (length(formula_interaction) > 0) stop("interactions not supported in univariate models")
       formula <- as.formula(paste(formula_outcome, paste(formula_independent, collapse = "+"), sep = "~"))
       formulas[[1]] <- list("id" = "", "type" = "multivariate", "formula" = formula)
       for (var in formula_independent) {