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-   -   Gene-level association test based on SNP data (http://seqanswers.com/forums/showthread.php?t=35118)

Sara-hc 11-06-2013 02:15 AM

Gene-level association test based on SNP data
 
Hi,

I've performed SNP calling from exome seq data followed by association testing (case-control), so I now have a p-value for each identified SNP.

I would like to some how summarise the p-values for SNPs identified in the same gene, so that I get a p-value for each gene (for use in downstream analysis).

So far I have been using the lowest p-value for each gene, but I wonder if this is really the best method..?

So, what is the preferred method for this? And are there any tools for doing this?

I hope someone can be helpful with this :)

Best regards,
Sara


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