Timothy Mak

In general, pseudovalidation is not very robust. It's based on a heuristic and its performance on real life datasets is unknown. Hence, I don't recommend it in general. I also...

Sorry for the late reply. Because of lack of time many of the functions in lassosum are still undocumented. Are there any specific features you would like better documentation?

Thanks for raising these issues. "Reference" stands for reference panel, and you can call it the LD panel if you like since yes, the LD is the main thing we're...

The issue of relatedness is a complicated one. As far as I know, the only substantial reference to this problem is Wray et al (2013, pitfalls of predicting complex traits...

lassosum doesn't use the plink convention of 1/2/-9 for case/control/missing. Using 1/2 instead of 0/1 should not affect results as the phenotype is only used for validation using correlation. However,...

By default lassosum uses the correlation as a measure of fit, and the best correlation achieved is given in the `best.validation.result` object within the list outputted from `validate()`. You can...

I mean is it possible to package all of steps 1-3 in https://montreal-forced-aligner.readthedocs.io/en/latest/installation.html#installing-from-source into a conda package? I was supposing that the current `conda install` more or less performs steps...

Will I need OpenGRM and OpenFST?

Actually, simply `conda install kaldi pynini` followed by `pip install .` doesn't work. First, I think you need `pip install -r requirements.txt`. But that didn't work for me either, as...

I used the default training config given [here for v2.0.0b7](https://montreal-forced-aligner.readthedocs.io/en/v2.0.0b7/user_guide/configuration/align.html#default-training-config-file) except with `subset` set to 0. ``` beam: 10 retry_beam: 40 features: type: "mfcc" use_energy: false frame_shift: 10 training: -...