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jrs95 / hyprcoloc

Hypothesis Prioritisation in multi-trait Colocalization
https://jrs95.github.io/hyprcoloc/
GNU General Public License v3.0
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hypRcoloc with 1500 phenotypes across 200 loci #14

Closed MalteThodberg closed 3 years ago

MalteThodberg commented 3 years ago

More of a question than an issue, but here we go:

I have run hypRcoloc on a dataset with ~1500 phenotypes measured on the same individuals. There are ~200 loci where at least 1 phenotype has genome-wide significant P-value < 5e-8. To make computations easier (/not crash my PC), for each loci, I extracted all phenotype with at least a suggestive P-value < 1e-6 and ran hypRcoloc with default parameters.

Results look pretty good, but I'm wondering about the priors: In the preprint, you run hyprcoloc in predefined LD-blocks. In my case, I run hypRcoloc at loci where I know at least one phenotype has significant signal.

Should I change prior.1 or prior.2 to something other than defaults in this case?

jrs95 commented 3 years ago

Hi Malte,

I think the default priors should be okay in your situation. @cnfoley anything to add here?

Best wishes,

James

cnfoley commented 3 years ago

Hi Malte,

With so many traits and regions, I think it would be sensible to assess sensitivity to the choice of priors. What I would do is:

  1. Run default analysis in each region
  2. (Within a region) For each cluster of colocalized traits identified - run a separate analysis assessing sensitivity to the default prior using the "sensitivity.plot". Section 3 in the vignette covers this.

If there are too many clusters for (2) to be pragmatically feasible let me know and I'll send you a function which avoids plotting. For this, you will have to input a 'decision rule' - deciding how much sensitivity to the prior (i.e. how sensitive the custer structure is to the prior) that you are willing to accept.

Good luck.

Chris

On Wed, Mar 10, 2021 at 8:40 PM James Staley @.***> wrote:

Hi Malte,

I think the default priors should be okay in your situation. @cnfoley https://github.com/cnfoley anything to add here?

Best wishes,

James

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