Commit 33202806 authored by Holger Brandl's avatar Holger Brandl
Browse files

used archive site for biomart

parent 2044674f
......@@ -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
......
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