used archive site for biomart

dge_workflow/featcounts_deseq_mf.R

@@ -472,10 +472,13 @@ geneInfo = quote({
   ## mart = biomaRt::useDataset("drerio_gene_ensembl", mart = biomaRt::useMart("ensembl"))§
 #  mart = biomaRt::useDataset(guess_mart(countData$ensembl_gene_id), mart = biomaRt::useMart("ensembl"))
     ## todo fix this https://support.bioconductor.org/p/74322/
-    mart = biomaRt::useDataset(guess_mart(countData$ensembl_gene_id), mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org"))
+    # mart = biomaRt::useDataset(guess_mart(countData$ensembl_gene_id), mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org"))
+    # mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = "dec2016.archive.ensembl.org", path = "/biomart/martservice", archive = FALSE)
+    mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL", dataset = guess_mart(countData$ensembl_gene_id), host = "dec2016.archive.ensembl.org", path = "/biomart/martservice", archive = FALSE)
 
-  c("ensembl_gene_id", "external_gene_name", "description", "chromosome_name", "start_position", "end_position") %>%
-        biomaRt::getBM(mart=mart)
+
+    c("ensembl_gene_id", "external_gene_name", "description", "chromosome_name", "start_position", "end_position") %>%
+        biomaRt::getBM(mart=mart) %>% tbl_df
 }) %>% cache_it("geneInfo")
 
 ## save as reference for downstream analysis