Timothy Mak

1. In theory it's best to use a LD panel that matches the population of the summary stats. However, that's often not available or doesn't have a large enough sample...

1. I just want to clarify that the tutorial is written by Sam and not me. In principle I don't recommend any reference panel over another, and it's the responsibility...

If it's really because of numerical issues, it's not something I can easily solve. It would be interesting to see if anyone else has come across this before. Otherwise, perhaps...

How many SNPs are there in each of the chromosomes? Have you made sure that these also exist in test.bfile? It sounds as if there are only a few SNPs.

The error message suggests that there are no SNPs left after matching the summary stats to test.bfile. It'd be difficult for me to figure out why without having your data....

If possible, could you try it with the example data attached with lassosum, provided in the directory here: `system.file("data", package="lassosum")`? Let us know the exact steps you took to obtain...

Hi @pmoulos As with the OP, why don't you try reproducing the results using the example data attached with lassosum? This would make it much clearer what the differences are....

Thanks for the detailed examples. I can confirm that the way snpStats reads the plink file, at least with the "as.numeric" conversion, is different from lassosum. (You can also try...

Finally there may also be very minor numerical differences due to the fact that lassosum performs the multiplication using C++, possibly at the same time as estimation, and may yield...

Not sure why you want to use pseudovalidate rather than simply correlating the generated phenotype with PRS. In general, pseudovalidation is deprecated in favour of splitvalidation. See the README.md for...