Import or compute PCA results — import

Imports PCA coordinates into `ggpop_pca`, or computes PCA using the optional `flashpcaR` backend. When `pop_group` is supplied, PCA plots map population groups to ggpop's unified discrete colour scale by default.

Usage

import_pca(file, type = c("auto", "plink", "gcta"), eigenval = NULL,
  pop_group = NULL, ...)
compute_pca(genotype, method = c("flashpca"), pop_group = NULL, ...)

Arguments

file: Path to a PLINK or GCTA eigenvector file.
type: Input format: `plink`, `gcta`, or `auto`.
eigenval: Optional eigenvalue file.
pop_group: Optional path or data frame with two columns, `sample` and `pop`, used for population colors.
genotype: Genotype matrix or flashpcaR-supported input.
method: PCA method. Currently `flashpca`, backed by `flashpcaR`.
...: Additional arguments.