search

chr1swallace / coloc

Repo for the R package coloc
142 stars 44 forks source link

Output SNP.PP.H3 from coloc.abf #47

Closed alxdrcirilo closed 2 years ago

alxdrcirilo commented 3 years ago

Hi there!

Thank you very much for this package. It's very convenient to use.

At the moment, I'm trying to have an additional column that would be the probability of H3 (i.e. SNP.PP.H3) per SNP. The coloc.abf function only outputs SNP.PP.H4. I tried looking into the source code (specifically the coloc.abf function and the combine.abf internal function) in an attempt to add some lines that would include the aforementioned column to my results, but alas, to no avail. Could you maybe help me with this or point me in the right direction? Any help would be greatly appreciated!

chr1swallace commented 3 years ago

Dear Alexandre,

the SNP.PP.H3 is a property of each pair of SNPs, and in fact isn't calculated directly.

What is it you wish to use the per SNP pair H3 probs for?

C

On Fri, 2021-03-19 at 02:02 -0700, Alexandre Cirilo wrote:

Hi there!

Thank you very much for this package. It's very convenient to use.

At the moment, I'm trying to have an additional column that would be the probability of H3 (i.e. SNP.PP.H3) per SNP. The coloc.abf function only outputs SNP.PP.H4. I tried looking into the source code (specifically the coloc.abf function and the combine.abf internal function) in an attempt to add some lines that would include the aforementioned column to my results, but alas, to no avail. Could you maybe help me with this or point me in the right direction? Any help would be greatly appreciated!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

alxdrcirilo commented 3 years ago

Hello Chris,

Thank you for the reply.

In essence, we would like to assess whether MR (Mendelian randomization), looking at methylation and nearby histone modification sites, could differentiate between these two epigenetic mechanisms. If they are instrumented by the same SNP (i.e. H4) then you would not expect differing results regardless of whether you intended to instrument methylation or histone modification. However, if we feel confident that the underlying causal variants are distinct (i.e. H3), then we may be able to use MR to establish whether methylation or histone modifications are on the causal pathway to our outcome.

May I ask how is the SNP.PP.H3 property extracted?

Looking forward to your feedback and thank you for your help!

Yining97 commented 3 years ago

Hi Chris,

Thanks for this great package! In fact, I was also looking for the way to extract posterior probability for each of the SNP under different hypothses (H3, etc.). Your answer would be much appreciated.

Look forward to your feedback!

chr1swallace commented 2 years ago

SNP.PP.H4 is already returned. SNP.PP.H4 is not calculated. But if you are confident in H3, I would simply finemap each dataset independently and take the posterior probabilities from that.