Title says most of it. I feel like hwe_normalized_pca could output the frequency it uses to center alongside the loadings. I’m doing this for downstream projection, which presumably is most of the use cases for outputting the loadings in the first place. Right now my process looks like: eig, score…

Since you’re likely filtering beforehand based on an AF annotation on the MatrixTable, I think it’s reasonable to use the generic PCA functionality with the HWE normalizing expression, so that the AF need not be recalculated, and then to annotate AF on the loadings from the rows of the MatrixTable. …

Or if this is really a common use case after running hwe_normalized_pca, we could consider adding AF to loadings as well, but only for that specialized PCA function.

Hi! I am following up on the thread about this subject on the hail chat: https://hail.zulipchat.com/#narrow/stream/123010-Hail-0.2E2.20support/topic/PCA.20projections.3F Using the 1K genome data and splitting this into two groups of the same samples but different variants: pca_mt = mt.filter_rows…

this is pretty old – the mt[row keys, :] syntax is deprecated. Instead use mt.rows()[row keys] or mt.index_rows(row keys)

@tpoterba and @konradjk Great, many thanks! pca_loadings = pca_loadings.annotate(pca_af = pca_mt.rows()[pca_loadings.locus, pca_loadings.alleles].pca_af) I also have a question about pc_project() function @konradjk , whether it is possible to use this (or something similar) to calculate the loadin…

If you have two separate tables with the same sample ids but disjoint variants, something like the following might be what you need. I generate two random datasets, mt1 and mt2. This model will generate the same loci for each dataset, so I shift the second dataset’s locus positions such that the da…

PCA to output allele frequencies alongside loadings?

Feature Requests

konradjk April 22, 2019, 4:24pm 6

We’ve updated pc_project to use the new syntax. The code lives here: https://github.com/macarthur-lab/gnomad_hail/blob/537cb9dd19c4a854a9ec7f29e552129081598399/utils/generic.py#L105

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PCA to output allele frequencies alongside loadings?

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