Error in format_snp_id(snp_id) in snp_readBGEN and snp_readBGI

privefl / bigsnpr

R package for the analysis of massive SNP arrays.

https://privefl.github.io/bigsnpr/

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Error in format_snp_id(snp_id) in snp_readBGEN and snp_readBGI #361

Closed JasperHof closed 2 years ago

JasperHof commented 2 years ago

Hello,

I have tried to load a BGI file in R, but I keep stumbling upon an error that I did not encounter in previous analyses. The head of my BGI file looks like this:

But when I try to load a subset of SNPs from the BGI file, my formatting seems to be wrong:

Also when I add the 'chr' part which is included in the chromsome column of the BGI file:

Is there something wrong with the formatting of the BGI file perhaps? The bgen file should be 8bits and of bgen version 1.2.

Any help is much appreciated!

privefl commented 2 years ago

I think you don't need to wrap snp_id with list().

JasperHof commented 2 years ago

Thank you for the suggestion! Unfortunately it is still not working if I leave out list(), for both options:

privefl commented 2 years ago

I see. This function just does not expect to have chrAB in the chromosome column (just AB). Can you change how BGI files are generated on your end? Otherwise, I would need to update the function to also allow for this.

JasperHof commented 2 years ago

I think so too. My first attempts at changing the BGI file today failed, will keep you posted..

JasperHof commented 2 years ago

Hi privefl,

The issue is now resolved by removing 'chr' from the chromosome column in the BGI file. Not sure how it got there.

Thanks again!