produce colored display of PCA of simple (putatively biallelic) genotypes from HPRC

produce colored display of PCA of simple (putatively biallelic) genotypes from HPRC

simplePCs(clvcf, particdf, pop = "super")

Arguments

clvcf

CollapsedVCF instance from VariantAnnotation

particdf

data.frame or tibble denoting populations etc. of HPRC participants

pop

character(1) "super" or "sub" to denote population type used to color points

Examples

data("smyd3v", package="BiocHPRClk")
data(hprc_partic)
simplePCs(smyd3v, hprc_partic)
#> Warning: variants with >1 ALT allele are set to NA
#> non-single nucleotide variations are set to NA
#> Warning: non-diploid variants are set to NA