Closed scienception closed 6 months ago
Hi,
Yes it's possible and your setup looks right (check doc). You'd use the same input flags as you would when computing burden masks (i.e. --set-list --anno --mask-def --aaf-bins
).
Cheers, Joelle
Thank you! Could you please point me to where this is done in the code? I was looking at this script but it seems just parsing rather than Pearson correlation computation. https://github.com/rgcgithub/regenie/blob/master/scripts/parseLD.r
check the documentation: https://rgcgithub.github.io/regenie/options/#ld-computation You would run this using the REGENIE software (that parseLD.r script is just to read the output binary file that contains the correlation information).
All right, I just wanted to know in which script the computation was done since the data isn't phased. Could you please send me the link to the script? I would appreciate it :) it is just for learning purposes. Thanks!
For example between geneA.M1.0.01 and geneA.M2.0.01? Where the former, for example, contains synonymous variants and the other missense variants.
What are the flags to be used? I am guessing
--compute-corr -ld-extract info.txt
But how does info.txt look like?
mask geneA.M1.0.01 geneA mask geneA.M2.0.01 geneA