PCA changes: no longer produces files, new --arrays option

[iris-garden]

Note

The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.

(Oct 13, 2016 at 18:29) tpoterba said:

PCA writes to annotations instead of files.

1. --scores [-s] option is required, defines sa path for the k sample PC scores
2. --loadings [-l] option is optional, defines va path for variant loadings (if this argument is not passed, pca will be a little faster)
3. --eigenvalues [-e] option is optional, defines global path for the k eigenvalues

The --arrays option produces Array[Double] for scores and loadings rather Struct{ PC1: Double, PC2: Double, PC3: Double, ...}

https://hail.is/commands.html#pca