Principal Component Analysis (PCA) on SNP genotype data

PCA for genotype data on the study server

ds.PCASNPS(
  gds,
  snp_subset = TRUE,
  prune = TRUE,
  ld.threshold = 0.2,
  datasources = NULL
)

Arguments

gds

character Name of the GDS object

prune

bool (default TRUE) TRUE to prune the GDS file using SNPRelate::snpgdsLDpruning

ld.threshold

Threshold for the pruning (see snpgdsLDpruning)

datasources

a list of DSConnection-class objects obtained after login.

Value

ggplot object with PCA plot (x axis First principal component; y axis Second principal component)