Principal Component Analysis (PCA) on SNP genotype data

PCA for genotype data on the study server

ds.PCA(
  genoData,
  snp_subset = TRUE,
  standardize = TRUE,
  ncomp = 5L,
  datasources = NULL
)

Arguments

genoData

character Name of the GenotypeData object on the server

snp_subset

bool (default TRUE) Use only SNPs that have been linked to ethnic groups

standardize

bool (default TRUE) Standardize the genotype data before performing the analysis

ncomp

integer (default 5L) Number of principal components to compute

datasources

a list of DSConnection-class objects obtained after login

Value

Returns list with the names of the objects created on the server side that will be used if the principal components are to be plotted

Details

Pooled method implemented using block method ("Parallel Algorithms for the Singular Value Decomposition." Berry et al. 2005). The `snp_subset` option uses gene regions that have been linked to ethnic groupings, it is suggested to use this option to optimize the computing time and get noise-less principal components.