Minor modifications (based on coding style).

R/create_design.R

@@ -218,7 +218,8 @@ create_design <- function(pheno_data, limma_parameters,
           clinical_cofactor <- factor(pheno_data[[cofactor_name]]) # nolint
           batches           <- factor(pheno_data[["Batch"]])
           genders           <- factor(pheno_data[["Gender"]])
-          design            <- stats::model.matrix(~ 0 + clinical + batches + genders + clinical_cofactor)
+          design            <- stats::model.matrix(~ 0 + clinical + batches + genders +
+                                                     clinical_cofactor)
           colnames(design)  <- c(levels(clinical),
                                  levels(batches)[2:length(levels(batches))],
                                  levels(genders)[2:length(levels(genders))],
@@ -254,7 +255,8 @@ create_design <- function(pheno_data, limma_parameters,
           clinical_cofactor <- factor(pheno_data[[cofactor_name]]) # nolint
           ages              <- as.numeric(pheno_data[["Age"]])
           genders           <- factor(pheno_data[["Gender"]])
-          design            <- stats::model.matrix(~ 0 + clinical + ages + genders + clinical_cofactor)
+          design            <- stats::model.matrix(~ 0 + clinical + ages + genders +
+                                                     clinical_cofactor)
           colnames(design)  <- c(levels(clinical), "Age",
                                  levels(genders)[2:length(levels(genders))], cofactor_name)
 
@@ -303,7 +305,8 @@ create_design <- function(pheno_data, limma_parameters,
           # We log information.
           rm(clinical_cofactor, ages, batches, genders)
           if (verbose == TRUE) {
-            message(paste0("[", Sys.time(), "] Design matrix created (pairs, ages, batches, genders)."))
+            message(paste0("[", Sys.time(),
+                           "] Design matrix created (pairs, ages, batches, genders)."))
           }
         }
       }

R/run_limma.R

@@ -51,11 +51,8 @@ run_limma <- function(pheno_data, eset, limma_parameters,
                       verbose            = FALSE) {
 
   # We extract the limma analysis parameters
-  clinical_factor <- limma_parameters[[1]]
   coefficients    <- limma_parameters[[2]]
   has_block       <- !is.null(cofactor_name)
-  clinical        <- factor(pheno_data[[clinical_factor]])
-  rm(clinical_factor)
 
   # We refine the prefix / suffic for the file names.
   if (file_prefix != "") {