Question: Phenotypic Variation Explained By Snps In Gwas
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gravatar for kumar.vinod81
6.5 years ago by
kumar.vinod81280
New Delhi
kumar.vinod81280 wrote:

Thanks Joey for answer of my last question. I am not getting how to calculate contribution of a set of significant SNPs to a particular trait. I calculated individual SNP contribution to a particular trait but if a number of SNPs contributing to the same trait then how to calculate the combined contribution of SNPs in explaining variation. Below some papers mentioned such analysis: http://www.nature.com/ng/journal/v42/n11/full/ng.695.html#/supplementary-information http://www.nature.com/ncomms/journal/v2/n9/full/ncomms1467.html (FIGURE 6) I've almost done all of the analysis like significant SNPs for all of the traits but I am totally confused at this step on SNP contribution to phenotypic variation. Can anyone please help? Thanks,

snp • 2.2k views
ADD COMMENTlink written 6.5 years ago by kumar.vinod81280
1

Sorry, but who's Joey and what was the last question?

ADD REPLYlink modified 6.5 years ago • written 6.5 years ago by Arun2.3k

I am not getting the exact answer of my question? I am working on GWAS in a diploid plant species with 6000 SNPs and 14 quantitative traits. I am able to get individual SNP contribution to a particular trait, but how to calculate contribution of a set of significant SNPs to a particular trait. I calculated individual SNP contribution to a particular trait but if a number of SNPs contributing to the same trait then how to calculate the combined contribution of SNPs in explaining variation. This paper (http://www.nature.com/ncomms/journal/v2/n9/full/ncomms1467.html (FIGURE 6) done the combined contribution of SNPs to trait. I've almost done all of the analysis like significant SNPs for all of the traits but I am totally confused at this step on SNP contribution to phenotypic variation. Can anyone please help? Thanks,

ADD REPLYlink written 6.5 years ago by kumar.vinod81280
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