Add host genes to differential expression results

Author: nictru

src/app.R

@@ -46,7 +46,7 @@ server <- function(input, output, session) {
   filtered_phenotype <- filterSamplesServer("filter_samples", phenotype)
   filtered_expression <- filterTranscriptsServer("filter_transcripts", circ_cpm, filtered_phenotype)
   dimredServer("dimred", filtered_expression, filtered_phenotype)
-  statisticsServer("statistics", filtered_expression, filtered_phenotype)
+  statisticsServer("statistics", filtered_expression, filtered_phenotype, circ_cpm)
 }
 
 shinyApp(ui = ui, server = server)

src/filter_transcripts.R

@@ -30,6 +30,7 @@ filterTranscriptsServer <- function(id, matrix, phenotype) {
   moduleServer(id, function(input, output, session) {
     matrixSamples <- reactive({
       cur_matrix <- matrix[, rownames(phenotype())]
+      cur_matrix$gene_id <- NULL
       cur_matrix
     })
 

src/load.R

@@ -17,7 +17,6 @@ loadCirc <- function() {
   circ <- read.table(circ_path, header = TRUE, sep = "\t")
   rownames(circ) <- circ$circ_id
   circ$circ_id <- NULL
-  circ$gene_id <- NULL
 
   return(circ)
 }

src/statistics.R

@@ -51,7 +51,7 @@ statisticsUI <- function(id) {
   )
 }
 
-statisticsServer <- function(id, expr_matrix, phenotype) {
+statisticsServer <- function(id, expr_matrix, phenotype, circ_cpm) {
   moduleServer(id, function(input, output, session) {
 
     output$column_select <- renderUI({
@@ -106,23 +106,26 @@ statisticsServer <- function(id, expr_matrix, phenotype) {
     })
 
     gene_results <- reactive({
-      test_result()[[1]]
+      results <- test_result()[[1]]
+      results[results$FDR < input$alpha, ]
     })
 
     circ_results <- reactive({
-      test_result()[[2]]
+      results <- test_result()[[2]]
+      results <- results[results$FDR < input$alpha, ]
+      annotated <- cbind(circ_cpm[rownames(results), ]$gene_id, results)
+      colnames(annotated)[1] <- "host_gene"
+      annotated
     })
 
     output$result_table_circ <- renderTable({
       results <- circ_results()
-      results <- cbind("circRNA" = rownames(results), results)
-      head(results)
+      cbind("circRNA" = rownames(results), results)
     })
 
     output$result_table_gene <- renderTable({
       results <- gene_results()
-      results <- cbind("gene" = rownames(results), results)
-      head(results)
+      cbind("gene" = rownames(results), results)
     })
   })
 }

test.R

@@ -7,5 +7,6 @@ phenotype <- loadPhenotype()
 control_samples <- rownames(head(phenotype))
 treatment_samples <- rownames(tail(phenotype))
 
-run(control_samples, treatment_samples)
+results <- run(control_samples, treatment_samples)
 
+print(head(results[[2]]))