--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DESeq_01.Rmd	Tue Feb 27 23:57:53 2018 -0500
@@ -0,0 +1,30 @@
+---
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = as.logical(opt$X_e),
+  error = TRUE
+)
+```
+
+# `DESeqDataSet` object
+
+```{r 'DESeqDataSet object'}
+count_file_paths = strsplit(opt$X_P, ',')[[1]]
+count_file_names = strsplit(opt$X_N, ',')[[1]]
+sample_table = read.table(opt$X_S, header = TRUE)
+row.names(sample_table) = sample_table[,2]
+sample_table = sample_table[count_file_names, ]
+
+## copy count files into OUTPUT_DIR/counts
+dir.create(paste0(OUTPUT_DIR, '/counts'), recursive = TRUE)
+file_copy = file.copy(count_file_paths, paste0(OUTPUT_DIR, '/counts/', count_file_names), overwrite = TRUE)
+
+## DESeqDataSet object
+dds = DESeqDataSetFromHTSeqCount(sampleTable = sample_table,
+                                 directory = paste0(OUTPUT_DIR, '/counts'),
+                                 design = formula(opt$X_p))
+dds
+```