@sjcrh/proteinpaint-server 2.98.2-1 → 2.99.0

package/utils/corr.R

@@ -19,7 +19,9 @@ coeffs <- c()
 pvalues <- c()
 sample_sizes <- c()
 for (i in 1:length(v1)) {
-    cor <- cor.test(as.numeric(unlist(v1[i])), as.numeric(unlist(v2[i])), method = input$method)
+    suppressWarnings({
+        cor <- cor.test(as.numeric(unlist(v1[i])), as.numeric(unlist(v2[i])), method = input$method)
+    })    
     coeffs <- c(coeffs, cor$estimate)
     pvalues <- c(pvalues, cor$p.value)
     sample_sizes <- c(sample_sizes, length(as.numeric(unlist(v1[i]))))
@@ -33,4 +35,4 @@ names(output)[2] <- "correlation"
 names(output)[3] <- "original_p_value"
 names(output)[4] <- "adjusted_p_value"
 names(output)[5] <- "sample_size"
-cat(paste0("adjusted_p_values:", toJSON(output)))
+toJSON(output)

package/utils/edge.R

@@ -19,7 +19,7 @@ read_json_time <- system.time({
     controls <- unlist(strsplit(input$control, ","))
     combined <- c("geneID", "geneSymbol", cases, controls)
 })
-cat("Time to read JSON: ", read_json_time[3], " seconds\n")
+#cat("Time to read JSON: ", read_json_time[3], " seconds\n")
 
 # Read counts data
 read_counts_time <- system.time({
@@ -59,7 +59,7 @@ read_counts_time <- system.time({
         stop("Unknown storage type")
     }
 })
-cat("Time to read counts data: ", read_counts_time[3], " seconds\n")
+#cat("Time to read counts data: ", read_counts_time[3], " seconds\n")
 
 # Create conditions vector
 conditions <- c(rep("Diseased", length(cases)), rep("Control", length(controls)))
@@ -69,19 +69,19 @@ gene_id_symbols <- paste0(geneIDs, "\t", geneSymbols)
 dge_list_time <- system.time({
     y <- DGEList(counts = read_counts, group = conditions, genes = gene_id_symbols)
 })
-cat("Time to generate DGEList: ", dge_list_time[3], " seconds\n")
+#cat("Time to generate DGEList: ", dge_list_time[3], " seconds\n")
 
 # Filter and normalize counts
 filter_time <- system.time({
     keep <- filterByExpr(y, min.count = input$min_count, min.total.count = input$min_total_count)
 })
-cat("Time to filter by expression: ", filter_time[3], " seconds\n")
+#cat("Time to filter by expression: ", filter_time[3], " seconds\n")
 
 normalization_time <- system.time({
     y <- y[keep, keep.lib.sizes = FALSE]
     y <- calcNormFactors(y, method = "TMM")
 })
-cat("Normalization time: ", normalization_time[3], " seconds\n")
+#cat("Normalization time: ", normalization_time[3], " seconds\n")
 
 # Differential expression analysis
 if (length(input$conf1) == 0) { # No adjustment of confounding factors
@@ -92,33 +92,33 @@ if (length(input$conf1) == 0) { # No adjustment of confounding factors
             })
         })
     })
-    cat("Dispersion time: ", dispersion_time[3], " seconds\n")
+    #cat("Dispersion time: ", dispersion_time[3], " seconds\n")
     
     exact_test_time <- system.time({
         et <- exactTest(y)
     })
-    cat("Exact test time: ", exact_test_time[3], " seconds\n")
+    #cat("Exact test time: ", exact_test_time[3], " seconds\n")
 } else { # Adjusting for confounding factors
     y$samples <- data.frame(conditions = conditions, conf1 = input$conf1)
     model_gen_time <- system.time({
         design <- model.matrix(~ conf1 + conditions, data = y$samples)
     })
-    cat("Time for making design matrix: ", model_gen_time[3], " seconds\n")
+    #cat("Time for making design matrix: ", model_gen_time[3], " seconds\n")
     
     dispersion_time <- system.time({
         y <- estimateDisp(y, design)
     })
-    cat("Dispersion time: ", dispersion_time[3], " seconds\n")
+    #cat("Dispersion time: ", dispersion_time[3], " seconds\n")
     
     fit_time <- system.time({
         fit <- glmFit(y, design)
     })
-    cat("Fit time: ", fit_time[3], " seconds\n")
+    #cat("Fit time: ", fit_time[3], " seconds\n")
     
     test_statistics_time <- system.time({
         et <- glmLRT(fit, coef = 2)
     })
-    cat("Test statistics time: ", test_statistics_time[3], " seconds\n")
+    #cat("Test statistics time: ", test_statistics_time[3], " seconds\n")
 }
 
 # Multiple testing correction
@@ -137,7 +137,7 @@ multiple_testing_correction_time <- system.time({
     names(output)[4] <- "original_p_value"
     names(output)[5] <- "adjusted_p_value"
 })
-cat("Time for multiple testing correction: ", multiple_testing_correction_time[3], " seconds\n")
+#cat("Time for multiple testing correction: ", multiple_testing_correction_time[3], " seconds\n")
 
 # Output results
-cat(paste0("adjusted_p_values:", toJSON(output)))
+toJSON(output)