make_yang_G_FBM: Yang method G matrix from a SNP big matrix

In hemstrow/GeneArchEst: Estimate Genomic Architecture for Quantitative Traits

Yang method G matrix from a SNP big matrix

Description

Make a G matrix using the method of Yang et al (2010) from a bigstatsr FBM (File-Backed Matrix). Uses code adapted from the AGH matrix package. Slower than simple vectorized code or the AGHmatrix function, but runs on huge genotype files in parallel without using huge amounts of memory.

Usage

make_yang_G_FBM(SNPmatrix, maf = 0.05, par = 1)

Arguments

SNPmatrix	File-backed matrix (FBM), where each row is an individual and each column is a loci. Values are the intergers 0, 1, or 2, where 0 and 2 are homozygotes and 1 is a heterozygote.
maf	numeric, default 0.05. Loci with minor allele frequencies below this will be removed.
par	numeric, default 1. Number of cores to use for calculations.

hemstrow/GeneArchEst documentation built on June 10, 2025, 5:06 a.m.