feat(PAB): lab script template

PAB_Lab13_diff_expr/Code/do_DE_analysis.r

@@ -0,0 +1,86 @@
+#!/usr/bin/Rscript --vanilla
+# author: hdescobarh
+
+########################## ENVIRONMENT SET UP ##########################
+
+args <- commandArgs(trailingOnly = TRUE)
+
+# Arguments validation
+
+if (length(args) < 2) {
+  stop("Need two arguments: input_file, output_directory.\n", call. = FALSE)
+}
+
+input_file_path <- args[1]
+output_directory_path <- args[2]
+
+if (!file.exists(input_file_path)) {
+  stop(sprintf("Input file (%s) does not exist", input_file_path))
+}
+
+if (!dir.exists(output_directory_path)) {
+  dir.create(output_directory_path)
+}
+
+# Libraries validation
+
+missing_packages <- character()
+for (package in c(
+  "edgeR"
+)) {
+  if (!require(package, quietly = TRUE, character.only = TRUE)) {
+    missing_packages <- append(missing_packages, package)
+  }
+}
+
+if (length(missing_packages) > 0) {
+  stop(
+    sprintf(
+      "Missing the following packages: %s",
+      paste(missing_packages, collapse = ", ")
+    ),
+    call. = FALSE
+  )
+}
+
+
+########################## LOAD AND VALIDATE DATA ##########################
+
+
+data <- read.table(
+  file = "Example_Data/Segemehl_filTotal3.txt",
+  header = TRUE, row.names = 1
+)
+
+# Table columns names verification
+
+if (!all(
+  grepl("[DM]\\d+R\\d+", colnames(data))
+)) {
+  stop(sprintf(
+    "Invalid columns names. They must follow the format '[DM]\\d+R\\d+'",
+    paste("", collapse = ", ")
+  ))
+}
+
+########################## ANALYSIS ##########################
+
+
+
+
+
+############ 2. Filtering
+
+
+############ 3. Data Normalization
+
+
+############ 4. Set experiment design
+
+
+############ 5. Dispersion estimation
+
+
+############ 6. Model fit
+
+############ 7. differential expression tests