G_mat: Calculate a genomic relationship matrix from marker...

In neyhartj/gws:

Calculate a genomic relationship matrix from marker information

Description

Calculates the genomic relationship matrix G using methods described by Van Raden (2008).

Usage

G_mat(
  X,
  base.pop = NULL,
  min.MAF = NULL,
  max.missing = NULL,
  impute.method = c("mean", "EM", "pass"),
  tol = 0.02,
  shrink = FALSE
)

Arguments

X	A matrix (n \times m) of marker data on n entries and m biallelic markers, coded as -1, 0, 1. Fractional (imputed) and missing values (NA) are allowed. Must have row (entry) names and column (marker) names.
base.pop	A character vector of entry names that make up the base population (i.e. unselected) for calculating marker allele frequencies (see Details).
min.MAF	See A.mat
max.missing	See A.mat
impute.method	The method for imputation. Can be "mean", "EM", or "pass". See rrBLUP[A.mat] for "mean" or "EM". If "pass", markers are assumed imputed.
tol	See A.mat
shrink	See A.mat

neyhartj/gws documentation built on Feb. 5, 2024, 12:42 a.m.