MungeSumstats
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Differentiate between errors and restricted datasets
Some OpenGWAS datasets don't show any data links on their website, I think because they're restricted use (at least currently). e.g. https://gwas.mrcieu.ac.uk/datasets/finn-b-G6_ALZHEIMER/
Currently, MungeSumstats
gives a message saying this this might be due to an incorrect ID or URL. However, it would be nice to let the user know it's simply restricted and won't be downloaded.
We could either do this:
- in the beginning of the
import_sumstats
step, or - the end of
find_sumstats
step, and provide a message to users that X, Y, Z GWAS were dropped from the results due to lack of accessibility (default). If so, we can add an arg to just show all results regardless of accessibility (non-default).
On that note, I think there is a way you can provide your OpenGWAS access token and get access to additional GWAS you've been authorized for. We just need to pass up the arg to supply the token to import_sumstats
.