get_kinship: Find a kinship matrix using the van Raden method.

In Alice-MacQueen/CDBNgenomics: Genomics Using the Cooperative Dry Bean Nursery Dataset

Description

Calculate the kinship matrix using code from GAPIT and bigsnpr and the methods of VanRaden (2009, J. Dairy Sci. 91:4414???C4423). This code is a modified version of the same code in GAPIT. Note that this matrix cannot currently be used with the GWAS methods in bigsnpr; however, this matrix could be used for other analyses, such as variance components analyses.

Usage

get_kinship(snp, ind.row = NA, hasInbred = TRUE, saveoutput = FALSE)

Arguments

snp	A "bigSNP" object; load with bigsnpr::snp_attach().
ind.row	An integer vector of the rows (individuals) to find a kinship matrix for. Defaults to all rows.
hasInbred	Logical. Does the SNP file contain inbred individuals or closely related individuals, like siblings? Default is TRUE.
saveoutput	Logical. Should the output be saved to the working directory?

Value

A kinship matrix with labeled rows and columns.

Examples

## Not run: 
K <- get_kinship(snp = snp, saveoutput = TRUE)

## End(Not run)

Alice-MacQueen/CDBNgenomics documentation built on Aug. 18, 2020, 4:39 p.m.