How is the odd ratio calculated? what's the background?

[Tao Wang]

Hi,

Could anyone explain a little how the odd ratio is calculated in giggle when query a file with Q intervals, against repeat file (e.g repeat_sort/rmsk.bed.gz) with N intervals. Suppose the overlap of Q and N is O. In the 2 by 2 table, how the estimate the n22 value, which is "number of intervals not in query file AND not in repeat file"? in the other word, what's the background?

If the query file contains GWAS SNPs, what's the background variants used?

Thanks!

Best,

Tao

[Ryan Layer]

Check out the 2nd paragraph on page 3:

https://www.biorxiv.org/content/biorxiv/early/2017/06/29/157735.full.pdf

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[Tao Wang]

Thanks for your refer!

If the query file only contains variants, should I set the genome size to the number of variants (, which is usually used in SNP enrichment)? otherwise the n22 would equal to genome_size/2 - n11 - n12 - n21. 

Best,

Tao

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[Ryan Layer]

I am afraid I cannot offer much advice here. In general, the GIGGLE score is useful for ranking search results and may not be a rigorous statistical measure.