issue with biomaRt ENSEMBL_MART_SNP
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Laurel ▴ 10
@0135d5a6
Last seen 12 weeks ago
United States

I have been having some issues accessing the SNP mart in biomart. I have been using the same script as in the biomart guide

snpmart = useEnsembl(biomart = "snp", dataset="hsapiens_snp”)


and it lets me see filter and attributes, and then when I try to run my query with getBM(), it tells me my mart doesn’t exist.

Error in martCheck(mart) :
You must provide a valid Mart object. To create a Mart object use the function: useMart.  Check ?useMart for more information.


I have been in contact with ensembl/biomart help support for weeks about this. Some blurbs of our exchanges:

# me to them
If I use the the Ensembl Gene mart, I can get output,
so something works, but we’re really hoping to use the Ensembl Variation
(SNP) mart. You can see I’ve tried a few different methods to get the mart
to work, and it just gets mad at me and says the error I mentioned below
when I run the final getBM command. The US East mirror I was using is
working now so that’s nice, but the mart is still non-cooperative. One of
the things I noticed is that when I tried the Ensembl Gene method (shown
as martthatworks), it gave me a size for the mart (like 1.4Mb or
something) and says Large Mart, whereas this just shows me “Formal mart
class” in the Rstudio description for the SNP mart. So it makes me wonder
if it’s not parsing the SNP mart well for some reason? I don’t know.

# from them to me
I've done a little more reading around and it looks like biomaRt is actually
pretty good about showing meaningful error messages, especially around
timeouts, e.g. https://support.bioconductor.org/p/9139740/. It sounds like the
package is built to understand the problems of running big, slow queries on
our biomarts. If your script isn't failing with an explicit "timed out"
message, it's probably not that.

Unfortunately, I'm still not sure what is going wrong, and I'm afraid there is
really no one here who understands biomarts (using them at least) and biomaRt
well enough to help. Could I suggest that you try contacting the biomaRt user
community? I know that the author of the package, Mike Smith, is very active
and very responsive. I'm sure he will be able to give you much more help than
we can.


I'm happy to provide more code for context, but basically, I can't seem to use this Mart object despite being able to use other Mart objects, and I would really love to do this analysis via R rather than the web interface as we will likely want to run it multiple times and an Rscript will be most convenient. Thanks so much for any insight or guidance.

biomaRt • 133 views
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Can you provide the full code you're running that produces the error? If you can run listAttributes() and listFilters() then your snpmart is a valid Mart object. Without seeing the exact code that you're running it's hard for me to provide much help. A minimal script that reproduces the problem would be of great help.