Gregor Gorjanc
Gregor Gorjanc
@petrelharp sorry for being pedantic, but `G^T s` gives you additive genetic (or breeding) values, not phenotypes. To get phenotypes we would have to add to `G^T s` at least...
So, two matvecs instead of a matmul and a matvec, right?
Is there a reason to focus on samples only? I would be interested in sums for ancestors too.
Yes, "partial" ancestral genomes/individuals will have only "partial" genetic values. In some cases ancestral genomes/individuals could be known in full, say in a simulation or in a pedigreed population, so...
> So: the output will be `out`, and suppose that the output for sample `v` is stored in `out[k[v]]`. @petrelharp what is k here?
Copying Slack discussion also here so we don’t loose it;) @jeromekelleher you asked what the other multiplication (pre- or left-multiplication) does. Let `G` be an `nSites x nSamples` matrix, `l`...
@jeromekelleher thinking a bit more about the “parsimony approach” you have taken. As you mentioned the nSamples*1 vector, with which you post multiply the genotype matrix, has to be “compressible”,...
> It's a very strong assumption @gregorgorjanc and it definitely won't hold in general. It's only going to work for things in which the underlying generative process is based on...
> Let `G` be an `nSites x nSamples` matrix, `l` be an `nSites x 1` vector, and `r` be an `nSamples x 1` vector. Just a note that in the...
Thinking about the usefulness of linear algebra operations with tree sequence ... One of key operations in data analysis is solving the least squares problem. There are many flavours of...