marker_pca: Perform PCA on marker data

Description Usage Arguments Details Value

View source: R/marker_pca.R

Description

Perform PCA on marker data

Usage

1
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 April 14, 2021, 7:04 p.m.