zilong-li / pcaone Goto Github PK

Hi!:) We'd love to try out PCAone, do you plan to create python bindings? Thank you!

Hi!

I am currently using PCAone on a fairly big dataset (195 samples, 4,2 million SNPs), and I get this warning:
WARNING: PCAone converged but the window size did not expand the whole data.
What would you recommend? Using a different algorithm?
I am using the last version of PCAone (v0.3.4) on a linux cluster.

Thanks for your help!

Doesn't the Eigen QR function construct a M x M matrix for the HouseholderQR?

The thin Q matrix is obtained like this for qr(G):
MatrixXd Q = qr.householderQ() * MatrixXd::Identity(m, t);

But then qr.householderQ() will be stored quickly in memory right? Or will most of the matrix just be un-initialized?

Hi Zilong,

I was quite interested in PCAone, since it supports several different algorithms and optimizations.

However, as with pcangsd, I feel the main drawback is that they do not support VCF files directly. Are there any plans to support VCF input? It would be nice if it would support genotypes, and both the GL and PL likelihoods (since different callers use different formats).

And maybe expand the Usage on the format of the output file and how you can make a plot out of it. Is it the same format as pcangsd?

thanks,

PS - if your plan is to have it be a standard for bio/popgen research, it could be a good idea to add it to bioconda. 😄