ds.PCA: Principal Component Analysis (PCA) on SNP genotype data

In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association functions.

Principal Component Analysis (PCA) on SNP genotype data

Description

PCA for genotype data on the study server

Usage

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

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.

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

isglobal-brge/dsOmicsClient documentation built on March 20, 2023, 3:52 p.m.