af {lfa} | R Documentation |
Compute matrix of individual-specific allele frequencies
af(X, LF, safety = FALSE)
X |
a matrix of SNP genotypes, i.e. an integer matrix of 0's, 1's, and 2's. Sparse matrices of class Matrix are not supported (yet). |
LF |
Matrix of logistic factors, with intercept. Pass in the
return value from |
safety |
optional boolean to bypass checks on the genotype matrices, which require a non-trivial amount of computation. |
Computes the matrix of individual-specific allele
frequencies, which has the same dimensions of the genotype matrix.
Be warned that this function could use a ton of memory, as the
return value is all doubles. It could be wise to pass only a
selection of the SNPs in your genotype matrix to get an idea for
memory usage. Use gc
to check memory usage!
Matrix of individual-specific allele frequencies.
LF = lfa(hgdp_subset, 4) allele_freqs = af(hgdp_subset, LF)