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JEFworks-Lab / HoneyBADGER

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
http://jef.works/HoneyBADGER/
GNU General Public License v3.0
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error when connecting to BioMart #25

Closed HaotengYan closed 5 years ago

HaotengYan commented 5 years ago

HI I got an error when I tried to run HoneyBADGER using the example data:

Request to BioMart web service failed. The BioMart web service you're accessing may be down. Check the following URL and see if this website is available: http://jul2015.archive.ensembl.org:80/biomart/martservice type=registry&requestid=biomaRt Error in if (!grepl(x = registry, pattern = "^\n*")) { : argument is of length zero

It seems like something goes wrong when I connect to BioMart. Do you have any advice on solving this problem? Many thanks!

JEFworks commented 5 years ago

Hi Haoteng,

It looks like BioMart may just have been temporarily down or the proxy that is used in the tutorial may have been down. I just tried and it seems like BioMart is back up. Please try again.

You can always try a different host if it's a host-specific issue: https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html As you've seen from the tutorial, HoneyBADGER uses the BioMart object to pull out each gene's chromosome, start, and end positions that's in your expression matrix. If you want to combine with the allele-based model, the coordinates of these start and end positions will need to match up so you will want to make sure the human reference genome version from BioMart matches the one you used for your alignment.

Hope that helps, Jean

HaotengYan commented 5 years ago

Thank you for your kindly reply. This problem seems to be solved.