Question

Find LD blocks

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8.8 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 • 3.0k views

ADD COMMENT • link updated 16 months ago by Ram 43k • written 8.8 years ago by erezts • 0

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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

ADD REPLY • link updated 16 months ago by Ram 43k • written 8.8 years ago by erezts • 0

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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!

ADD REPLY • link updated 16 months ago by Ram 43k • written 8.8 years ago by alesssia ▴ 580

score 1 · Answer 1 · 2015-06-22

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8.8 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?

ADD COMMENT • link 8.8 years ago by alesssia ▴ 580