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Improve synonymous RSID detection #44

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bschilder opened this issue Apr 28, 2021 · 1 comment
Open

Improve synonymous RSID detection #44

bschilder opened this issue Apr 28, 2021 · 1 comment
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enhancement New feature or request

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@bschilder
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echolocatoR matches the GWAS sum stats with the LD ref panel based on SNP RSIDs. However, some SNPs have multiple synonymous RSIDs (e.g. from different version of dbSNP).

To improve overlap, I'd like to add a function that looks for overlap not just between the given RSIDS, but all their synonyms too.
@bschilder bschilder added the enhancement New feature or request label Apr 28, 2021
@bschilder bschilder self-assigned this Apr 28, 2021
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For GWAS sumstats, MungeSumstats does a nice job of standardising RSIDS.

But other data sources, like LD panels, may still not match up.
orthogene::map_genes might be helpful for this as it can take RSIDS as well.

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enhancement New feature or request
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🦇🦇 echoverse 🦇🦇
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