SeqVarTools (version 1.10.0)

pca: Principal Component Analysis

Description

Calculates the eigenvalues and eignevectors of a SeqVarGDSClass object with Principal Component Analysis

Usage

"pca"(gdsobj, eigen.cnt=32)

Arguments

gdsobj

A SeqVarGDSClass object with VCF data.

eigen.cnt

An integer indicating how many eigenvalues and eignvectors to return.

Value

A list with two elements:

eigenval

A vector of length eigen.cnt with eigenvalues

eigenvect

A matrix of dimension ("selected samples", eigen.cnt).

Details

Calculates the genetic covariance matrix and finds the eigen decomposition.

References

Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genetics 2:e190.

See Also

SeqVarGDSClass, applyMethod

Examples

gds <- seqOpen(seqExampleFileName("gds"))
pca <- pca(gds)
pca$eigenval
head(pca$eigenvect)
seqClose(gds)