marker_pca: Perform PCA on marker data

In etnite/bwardr: Brian Ward personal R package

Perform PCA on marker data

Description

Perform PCA on marker data

Usage

marker_pca(geno, snps = "rows")

Arguments

geno	A matrix of SNP data with SNPs in minor-allele dosage format: 2 = homozygous for minor allele 1 = heterozygous 0 = homozygous for major allele NA = missing data
snps	Either "rows" to indicate that SNPs are in rows and individuals are in columns, or "cols" to indicate the SNPs are in columns and individuals are in rows

Details

This function performs a "quick and dirty" principle component analysis on the input matrix of SNP data. A genetic relationship matrix is calculated first, and then an Eigen decomposition is performed on this matrix

Value

The Eigen decomposition of the input genotypic matrix

etnite/bwardr documentation built on Jan. 6, 2023, 7:12 a.m.