added temporary notes

rioualen · Jun 2, 2016 · 5223eab · 5223eab
1 parent e4185c4
commit 5223eab
Showing 1 changed file with 14 additions and 0 deletions.
diff --git a/scripts/snakefiles/rules/download_from_GEO.rules b/scripts/snakefiles/rules/download_from_GEO.rules
@@ -21,6 +21,20 @@ rule download_sra:
 """
 
 
+## TODO ! download function
+
+## 1. Get SRR ids from GSE id
+
+library(GEOquery)
+gse <- getGEO('GSE20870') # retrieves a GEO list set for your SRA id.
+## see what is in there:
+show(gse)
+# There are 2 sets of samples for that ID
+##  what you want is table a with SRR to download and some sample information:
+## lets see what the first set contains:
+df <- as.data.frame(gse[[1]])
+write.csv(df, file="test.csv")
+head(df)