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kkdey / GSSG

Gene Set + S2G strategy annotations analyzed for disease architecture
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how to get the SNP numbers？ #10

Closed bitcometz closed 3 years ago

bitcometz commented 3 years ago

hello， I found in your paper : image

and the number 5,961,159 was also used in your R: https://github.com/kkdey/GSSG/blob/master/code/ldsc/ldsc_postprocess_enrichment.R

Could you tell me how this number was obtained ？

Best

kkdey commented 3 years ago

This number is the total number common SNPs (not low frequency) used to compute the heritability and is smaller than the overall size of the annotation of ~10 mil that contains both common and low freq variants.

bitcometz commented 3 years ago

Dear kkdey, thanks for your reply !!! So is it the same for each time when I used different gene sets (got from expression compares). Or should I look into the output log files and get the numbers ?

Thanks !!!

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kkdey commented 3 years ago

Yes it would be the same each time across gene sets and traits, as it pertains to computing the overall heritability.

bitcometz commented 3 years ago

Thanks ！！！