compute_gene_pcs: Compute principal components of SNPs annotated to genes.
In SimonLarsen/higana: Ontology-based analysis of genetic variants.

Compute principal components of SNPs annotated to genes.

compute_gene_pcs(
  path,
  data,
  stand = "binom2",
  explain_var = 0.95,
  max_pcs = 50,
  num_parts = 1,
  rsvd_threshold = Inf
)

`path`	Path to output file.
`data`	A `BEDData` object.
`stand`	Which standardization method to use. One of "none", "binom" (old Eigenstrat-style), "binom2" (new Eigenstrat-style), "sd" (zero-mean unit-variance) or "center" (zero mean).
`explain_var`	Restrict number of PCs to explain at least this fraction of variance.
`max_pcs`	Return at most this number of PCs.
`num_parts`	Number of parts to write output to.
`rsvd_threshold`	Use randomized SVD when number of variables exceeds this threshold.