cofactor.pca.cor: Correlation between cofactors and principal components.

In rachael-kane/GLM2020: GWAS using GLM

Description

Test for correlations between user-specified cofactors and principal components calculated from genotype data. Automatically remove principal components linearly dependent (correlated) with user-specified cofactors.

Usage

cofactor.pca.cor(U, G)

Arguments

U	A numeric matrix containing user-specified cofactors. Dimensions are n rows (individuals) by t columns (cofactors).
G	A numeric matrix containing genotype data. Dimensions are n rows (individuals) by m columns (genetic markers).

Details

When U is unspecified, cofactor.pca.cor will return a list of 1 object. With U unspecified, function will carry out principal components analysis identically to the native R function prcomp(), and cofactor.pca.cor will return principal components scores in $cov. $cov is a numeric matrix containing all principal components and individual scores. Dimensions are n rows (individuals) by t columns (principal components).

When U is specified, cofactor.pca.cor will return a list of 3 objects. $orig_pc is a numeric matrix containing all original principal components and individual scores. $cov is a numeric matrix containing user-specified cofactors and all principal components not correlated with the user-specified cofactors. Dimensions are n rows (individuals) by t columns (cofactors). $removed is a character matrix indicating which principal components were removed.

The $cov matrix is intended for use as the "C" argument in the GWASbyGLM function included in this package.

Type vignette("GLM2020_tutorial") for example use.

Value

A list of 1 or 3 objects.

U unspecified: 1 object. $cov, a numeric matrix containing all principal components and individual scores.

U specified: 3 objects. $orig_pc, a numeric matrix containing all original principal components $cov, a numeric matrix containing user-specified cofactors and retained principal components. $removed, a matrix indicating which principal components were removed.

rachael-kane/GLM2020 documentation built on March 31, 2020, 12:51 a.m.