Question: Estimating Variance Explained By Snps
3
gravatar for Purpleone
8.6 years ago by
Purpleone90
Australia
Purpleone90 wrote:

What is a standard approach to estimating the (phenotypic) variance explained by SNPs in a case/control GWAS?

I know about GCTA, but it's very computationally intensive. Are there simpler methods?

snp • 3.7k views
ADD COMMENTlink written 8.6 years ago by Purpleone90
0
gravatar for Philipp Bayer
8.5 years ago by
Philipp Bayer6.8k
Australia/Perth/UWA
Philipp Bayer6.8k wrote:

You can do regressions in PLINK: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml

I did a small GWAS recently using a logistic regression for a binary phenotype in roughly 300 subjects and that took 2 seconds.

ADD COMMENTlink written 8.5 years ago by Philipp Bayer6.8k

Do plink also feasible for plant quantitative traits or it works only for binary phenotypes. I've tried with PLINK but at last in a unsuccessful manner. I want to try with it to confirm my GAPIT results but not finding a good way to analysis. Thanks

ADD REPLYlink written 7.6 years ago by kumar.vinod81280
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