Non-European populations

[irisjansen]

Hi!

Thank you for this great R package, it really is of great value. One aspect that I am missing (or what I am not understanding correctly) is to munge sumstats of non-European populations. So it would be possible to do the same allele frequency checks as for the European populations. Could I already accomplish this by setting a certain option? Or maybe it is something that you are planning to implement?

Thank you in advance!

Best wishes,
Iris

[Al-Murphy]

Hey!

Great to hear you are finding it useful! So the allele frequency checks are based on the frequency values in the sumstats itself (rather than from some reference database). Therefore, whatever population was used for the GWAS itself will be used. I believe this is the most accurate way as it avoids issues where the wrong frequencies are used down to an incorrect ancestry. As far as I know, there is actually no reference database of frequencies of SNPs based on different ancestries in R and even if there was, checking the frequency based on this may not be wise (based on what I said above).

Check out the check_freq() function if you want to see an example of the usage but basically it uses the column FRQ in the dataset. To see what columns can map to this have a look at the mapping file data("sumstatsColHeaders").

Hope this helps?

Thanks,
Alan.

[irisjansen]

Hi Alan,

Thank you for your fast reply, and yes this definitely helps!

Best,
Iris

[Al-Murphy]

Great! Feel free to reopen this issue if you have any further questions on it.

Thanks,
Alan.