Find LD blocks
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8.7 years ago
erezts • 0

Hello everybody,

I was looking for a proxy for a certain SNP and couldn't find one (using SNAP, ENSEMBLE). Therefore I would like to look for an LD block which contains my SNP and other SNPs that might be used as good proxies. Anyone knows good tools for that?

Thanks,

Erez

SNP gene sequencing • 2.9k views
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Thanks for that alessia.

I'm not proficient with R so I was hoping for a database or a tool that can do it

Erez

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This is a tool that is doing it! Read how the function works at page 7: http://cran.r-project.org/web/packages/rsnps/rsnps.pdf You need to know a very little R to have it working!

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8.7 years ago
alesssia ▴ 580

rsnps R package (http://cran.r-project.org/web/packages/rsnps/index.html) has a function called "LDSearch" that searches for SNPs in Linkage Disequilibrium with a set of SNPs given as input. May this help?

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