Timothy Mak

There's some explanation of it in the Genetic Epi paper. However, I believe in most cases, using splitvalidate is preferable.

lassosum and plink are not doing the same thing so I don't understand why you would expect the same result from lassosum and plink.

What do you mean by adjusted beta? From your code, you have generated beta by beta

Can you explain what you mean by "adjusted beta" and how it is supposed to differ from "beta"?

If `X` denote the test genotype matrix, then `v$best.pgs` = `X %*% v$best.beta`, which is the "adjusted beta" you described. It could be different from what you get from plink...

@dheerajbobbili1988 , Yes. If `out` is the output from the `lassosum.pipeline()` function, then the `out$sumstats` object is a data.frame which gives the details of the SNPs used in `v$best.beta`. You...

Incidentally, if you know the A1,A2 of the bfile is the same as that in `test.bfile`, you can use `pgs(test.bfile, v$best.beta)` to generate the PGS also. The `pgs` function also...

Can you give me your entire script?

So are you still getting this error `splitvec.from.bfile(bfile) : length(pvec) == length(bfile) is not TRUE`. And if so, at which stage?

Yes, calculating PGS can take a long time with a large sample size. One way to speed up the calculation is to use multiprocessing (see [here](https://github.com/tshmak/lassosum#parallel-processing-with-the-parallel-package)). Another way is to...