Genomic Relationship Calculation
This function calculates a genomic relationship matrix following the method decribed by Yang et al (2010)
stamppGmatrix(geno)
geno |
a data frame containing allele frequency data generated from stamppConvert, or a genlight object containing genotype data, individual IDs, population IDs and ploidy levels |
An object of class matrix which contains the genomic relationship values between each individual
Luke Pembleton <luke.pembleton at agriculture.vic.gov.au>
Yang J, Benyamin B, McEvoy BP, et al (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42, 565-569. <doi:10.1038/ng.608>
# import genotype data and convert to allele frequecies data(potato.mini, package="StAMPP") potato.freq <- stamppConvert(potato.mini, "r") # Calculate genomic relationship values between each individual potato.fst <- stamppGmatrix(potato.freq)
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