grm.matrix {rres}

GRM for multiple individuals

Description

grm.matrix computes relatedness estimates between every pairs of individuals.

Usage

grm.matrix(genotype, freq, method = "twostep", weights = NULL,
  init.est = NULL)

Arguments

genotype

numeric matrix.

freq

numeric vector, values between 0 and 1.

method

string.

weights

numeric vector, values between 0 and 1.

init.est

numeric.

Details

genotype is the matrix of counts of reference alleles. Rows represents subjects and columns represents SNP markers. freq is the vector of reference allele frequencies.

The default method is "twostep", other options include "classic", "robust" and "general". When using the default "twostep" method, user can supply an initial estimate through init.est to bypass the first step. When "general" is selected, weights must also be specified. The difference between the two-step GRM, classic GRM and robust GRM is discussed in Wang et al. (2017).

References

Wang et al. (2017) Genetics 205:1063-1078, https://www.ncbi.nlm.nih.gov/pubmed/28100587.

See Also

grm.pair.