Correlation ldref example vs main tutorial/vignette about paper-ldpred2 HOT 3 CLOSED

The provided LD ref has many advantages, and you should prefer using it.

The main reason why you should not use it is when you do not have imputed data and the overlap between your test data and the LD ref is not great.

The second main reason is when you're building PGS using GWAS from another ancestry.

from paper-ldpred2.

Thank you for your response! I'm so sorry for my confusion.

Once I use the ldref correlation code, can I just continue with the code in the tutorial for LDpred2-auto? It appears to run properly but I want to ensure I am calculating the right thing. Does the code in the example with ldref also deal with summary stats QC or does that need to be done separately?

Additionally, is the number of variants used to calculate the pred score represented by the number of observations within df_beta?

Thank you so much again,
Kate

from paper-ldpred2.

Sumstats QC needs to be performed before.

Yes, all variants you have as input (in df_beta and corr) will be used.

from paper-ldpred2.