admix_prop_indep_subpops {bnpsd} | R Documentation |
This function constructs an admixture proportion matrix where every individuals is actually unadmixed (draws its full ancestry from a single intermediate subpopulation).
The inputs are the vector of subpopulation labels labs
for every individual (length n
), and
the length-k
vector of unique subpopulations subpops
in the desired order.
If subpops
is missing, the sorted unique subpopulations observed in labs
is used.
This function returns the admixture proportion matrix, for each individual 1 for the column corresponding to its subpopulation, 0 otherwise.
admix_prop_indep_subpops(labs, subpops = sort(unique(labs)))
labs |
Length- |
subpops |
Optional length- |
The n
-by-k
admixture proportion matrix.
The unique subpopulation labels are given in the column names.
# vector of subpopulation memberships labs <- c(1, 1, 1, 2, 2, 3, 1) # admixture matrix with subpopulations (along columns) sorted admix_proportions <- admix_prop_indep_subpops(labs) # declare subpopulations in custom order subpops <- c(3, 1, 2) # columns will be reordered to match subpops as provided admix_proportions <- admix_prop_indep_subpops(labs, subpops) # declare subpopulations with unobserved labels subpops <- 1:5 # note columns 4 and 5 will be false for all individuals admix_proportions <- admix_prop_indep_subpops(labs, subpops)