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.