Transform coancestry matrix to kinship matrix
If Theta is the coancestry matrix and Phi is the kinship matrix (both are n-by-n symmetric), then these matrices agree off-diagonal, but the diagonal gets transformed as
diag( Phi ) = ( 1 + diag( Theta ) ) / 2.
coanc_to_kinship(coancestry)
coancestry |
The |
The n-by-n kinship matrix, preserving column and row names.
The inverse function is given by \link[popkin]{inbr_diag}.
# a trivial case: unadmixed individuals from independent subpopulations # number of individuals/subpops n_ind <- 5 # unadmixed individuals admix_proportions <- diag(rep.int(1, n_ind)) # equal Fst for all subpops inbr_subpops <- 0.2 # diagonal coancestry matryx coancestry <- coanc_admix(admix_proportions, inbr_subpops) kinship <- coanc_to_kinship(coancestry) # a more complicated admixture model # number of individuals n_ind <- 5 # number of intermediate subpops k_subpops <- 2 # non-trivial admixture proportions admix_proportions <- admix_prop_1d_linear(n_ind, k_subpops, sigma = 1) # different Fst for each of the k subpops inbr_subpops <- c(0.1, 0.3) # non-trivial coancestry matrix coancestry <- coanc_admix(admix_proportions, inbr_subpops) kinship <- coanc_to_kinship( coancestry )
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