ds.PCASNPS: 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.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)

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