Question about direction in tutorial#parameters

[Siyi Liu]

Hi Tanya,

Thanks for maintaining this forum.

I would like to ask about the description of the direction for Maximum GWAS P-value.  As is stated in the SNP2GENE page, setting this parameter to 1 would include all SNPs in LD with the lead SNP for annotation (as candidate SNPs); Hence, the higher parameter should increase the number of candidate SNPs, not decrease it. Similarly, in the section of eQTL mapping, a lower eQTL maximum p-value (more strict) should produce fewer mapped genes. I would like to know if my interpretation is correct, or if it was a typo on the website?

Thanks for your time and patience.

Best regards,

Siyi

[Tanya Phung]

Hi Siyi,

Could you please be more specific? Can you include the screenshots of which parameters you were mentioning? 

Best,
Tanya

[Siyi Liu]

Hi Tanya,

Thanks for replying.

Absolutely! Here are the screenshots of the parameters I'm confused about.

I would expect that a higher Maximum GWAS P-value threshold would increase the number of candidate SNPs.

Similarly, a lower maximum P-value (e.g., 5e-10, extremely strict) would result in fewer eQTLs and mapped genes.

Best Regards,

Siyi

[Tanya Phung]

Hi Siyi, 

Thank you for the screenshots. 

I think that you are correct, and that the direction in the tutorial might be a typo. 

I will need to double-check this again, and will make adjustment to the tutorial in the next update. 

Best,
Tanya

[Siyi Liu]

Hi Tanya,

Thanks for replying. I'm glad I could be helpful. Looking forward to the next update.

Best wishes,

Siyi

[Tanya Phung]

Hi Siyi, 

I confirmed your findings with running a few test jobs. 
Using the example input file and: 

- default gwas P, which is 0.05 resulted in 1247 candidate SNPs

- gwas P threshold of 0.5 (which is higher) resulted in 1248 candidate SNPs (more)

- default eQTLs p threshold of 1e-3, using the 3 blood tissues from GTEx, resulted in 336 mapped genes

- eQTLs threshold of 1e-5 (which is lower) resulted in 275 mapped genes (fewer)

I updated the tutorial accordingly. 

Best,
Tanya