Significance testing of top vs. random SNPs
0
0
Entering edit mode
8 months ago
am29 ▴ 30

After performing GWAS, I calculated the percentage of phenotypic variance (SNP-based heritability) for top SNPs and random SNPs using GREML (GCTA). The variance of random SNPs was calculated for 3 different groups of randomly chosen SNPs and then averaged to get the final result. Top SNPs explained much more variance then random (10% > 0.2%). I want to check if the difference is statistically significant.

Which significance test should I use for this?

SNPs significance variance statistical • 434 views
ADD COMMENT
1
Entering edit mode

I suspect there is a more appropriate way, but you could do a permutation analysis, randomly sampling n SNPs 1000 times and generate a one-tailed p-value (where n is the number of SNPs in your top SNPs group). If your variance is above 990 of the random permutations then your p-value is 0.01.

I would also recommend using a circular genomic permutation analysis which accounts for genomic proximity and structure of outliers when conducting a permutation analysis as described in Cabrera et al. 2012.

ADD REPLY

Login before adding your answer.

Traffic: 2253 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6