diff DESeq.Rmd @ 3:a520a6c5e111 draft default tip

update

--- a/DESeq.Rmd	Tue Feb 27 14:07:10 2018 -0500
+++ b/DESeq.Rmd	Tue Feb 27 15:30:28 2018 -0500
@@ -24,12 +24,13 @@
 row.names(sample_table) = sample_table[,2]
 sample_table = sample_table[count_file_names, ]
 
-## copy count files into working directory
-file_copy = file.copy(count_file_paths, count_file_names, overwrite = TRUE)
+## 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 = './',
+                                 directory = paste0(OUTPUT_DIR, '/counts'),
                                  design = formula(opt$X_p))
 dds
 ```
@@ -88,9 +89,9 @@
 dds <- DESeq(dds)
 ```
 
-```{r}
-rm("opt")
-save(list=ls(all.names = TRUE), file=opt$X_w)
+```{r echo=FALSE}
+# save objects except for opt.
+save(list=ls()[ls() != "opt"], file=opt$X_w)
 ```