visualize PCA colored by populations for a selected SuperPopulation

visualize PCA colored by populations for a selected SuperPopulation

viewStrat1KG(
  pcs,
  selectedPCs = 1:4,
  superpop = "AFR",
  superOnly = FALSE,
  dropNAs = TRUE
)

Arguments

pcs

matrix of principal components, assumed to have colnames PC[1,...] typically PC1-PC10

selectedPCs

numeric(), values typically drawn from 1:10

superpop

character(1)

superOnly

logical(1) defaults to FALSE; if TRUE, do not limit to one superpopulation

dropNAs

logical(1) defaults to TRUE

Note

Population and SuperPopulation definitions are at `https://www.internationalgenome.org/data-portal/population`, mapping from sample to population/superpopulation is available via `BiocHail::path_1kg_annotations`.