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gkichaev / PAINTOR_V3.0

Fast, integrative fine mapping with functional data
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Annotation correlation #36

Open pwh124 opened 5 years ago

pwh124 commented 5 years ago

Hello,

In the WIKI for PAINTOR, it states:

After obtaining the output for all of the annotations marginally, prioritize annotations based on the improvement in the model fit. Take the top annotations (usually no more than 4 or 5) to enter the final model that are roughly uncorrelated with one another. We recommend correlation matrices for this process.

My annotations are BED files... how would I go about checking to see if they are correlated?

Many thanks, Paul

ppericard commented 5 years ago

Hi,

I'm really interested in an answer because I was having the same question. I also came to me that the wiki could be talking about computing correlation matrices between the final SNPs posterior probabilities for these individual annotation runs. Either way I'm really interested in an answer.

Thanks in advance

pwh124 commented 5 years ago

All,

I emailed Dr. Pasaniuc and (quickly) received the following answer:

You would first annotate snps with the bed files (there should be a script that does that) and second you can correlate the two vectors corresponding to those annotations. A squared correlation smaller than 0.2 is usually ok.

After doing some snooping, Pearson correlation should work for this.