@sjcrh/proteinpaint-server 2.108.0 → 2.109.0

package/src/bedj.parseBed.js

@@ -69,7 +69,7 @@ to parse line as gene file, require following:
 
 */
 
-import checkReadingFrame from './checkReadingFrame'
+import checkReadingFrame from './checkReadingFrame.js'
 
 //a valid exonFrames field can only contain members of validFrames, names -1, 0, 1, or 2
 const validFrames = new Set(['-1', '0', '1', '2'])

package/src/run_R.js

@@ -11,7 +11,7 @@ Standard output of the R script is returned.
 */
 
 import fs from 'fs'
-import serverconfig from './serverconfig'
+import serverconfig from './serverconfig.js'
 import { spawn } from 'child_process'
 import { Readable } from 'stream'
 

package/utils/edge.R

@@ -30,13 +30,6 @@ filter_genes_by_global_variance <- function(read_counts, gene_id_symbols, num_va
    return(list(read_counts = read_counts, gene_id_symbols = gene_id_symbols))
 }
 
-# Will implement this later
-filter_genes_by_group_variance <- function(read_counts, gene_id_symbols, num_variable_genes, cases, controls) {
-    # Divide the read counts into two groups
-    case_read_counts <- read_counts[, cases]
-    control_read_counts <- read_counts[, controls]
-}
-
 # Read JSON input from stdin
 read_json_time <- system.time({
     con <- file("stdin", "r")
@@ -146,15 +139,29 @@ if (length(input$conf1) == 0) { # No adjustment of confounding factors
     # Check the type of confounding variable
     if (input$conf1_mode == "continuous") { # If this is float, the input conf1 vector should be converted into a numeric vector
       conf1 <- as.numeric(input$conf1)
-    } else { # When input$conf1_mode == "discrete" keep the vector as string. PLEASE ASK WHAT OTHER POSSIBLE TERM TYPES ARE POSSIBLE
+    } else { # When input$conf1_mode == "discrete" keep the vector as string.
       conf1 <- as.factor(input$conf1)
     }
 
-    y$samples <- data.frame(conditions = conditions, conf1 = conf1)
-    model_gen_time <- system.time({
-        design <- model.matrix(~ conditions + conf1, data = y$samples)
-    })
-    #cat("Time for making design matrix: ", model_gen_time[3], " seconds\n")
+    if (length(input$conf2) == 0) { # No adjustment of confounding factor 2
+          y$samples <- data.frame(conditions = conditions, conf1 = conf1)
+          model_gen_time <- system.time({
+                 design <- model.matrix(~ conditions + conf1, data = y$samples)
+          })
+          #cat("Time for making design matrix: ", model_gen_time[3], " seconds\n")
+    } else {
+          # Check the type of confounding variable 2
+          if (input$conf2_mode == "continuous") { # If this is float, the input conf2 vector should be converted into a numeric vector
+            conf2 <- as.numeric(input$conf2)
+          } else { # When input$conf2_mode == "discrete" keep the vector as string.
+            conf2 <- as.factor(input$conf2)
+          }
+          y$samples <- data.frame(conditions = conditions, conf1 = conf1, conf2 = conf2)
+          model_gen_time <- system.time({
+                 design <- model.matrix(~ conditions + conf1 + conf2, data = y$samples)
+          })
+          #cat("Time for making design matrix: ", model_gen_time[3], " seconds\n")
+    }
 
     dispersion_time <- system.time({
         y <- estimateDisp(y, design)
@@ -167,7 +174,7 @@ if (length(input$conf1) == 0) { # No adjustment of confounding factors
     #cat("Fit time: ", fit_time[3], " seconds\n")
 
     test_statistics_time <- system.time({
-        et <- glmLRT(fit, coef = 2)
+        et <- glmLRT(fit, coef = "conditionsDiseased")
     })
     #cat("Test statistics time: ", test_statistics_time[3], " seconds\n")
 }
@@ -192,3 +199,11 @@ multiple_testing_correction_time <- system.time({
 
 # Output results
 toJSON(output)
+
+#-----------------------------------#
+# Will implement this later
+filter_genes_by_group_variance <- function(read_counts, gene_id_symbols, num_variable_genes, cases, controls) {
+    # Divide the read counts into two groups
+    case_read_counts <- read_counts[, cases]
+    control_read_counts <- read_counts[, controls]
+}

package/utils/hwe.R

@@ -1,11 +0,0 @@
-library('hwde')
-
-con <- file("stdin","r")
-dat <- read.table(con,sep="\t",header=F,quote="")
-
-for (i in 1:nrow(dat)) {
-	pvalue <- hwexact( dat[i,1], dat[i,2], dat[i,3] )
-	cat(pvalue,"\n",sep="")
-}
-
-close(con)