af | R Documentation |

Compute matrix of individual-specific allele frequencies

af(X, LF, safety = FALSE, max_iter = 100, tol = 1e-10)

`X` |
A matrix of SNP genotypes, i.e. an integer matrix of 0's,
1's, 2's and |

`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.
Ignored if |

`max_iter` |
Maximum number of iterations for logistic regression |

`tol` |
Numerical tolerance for convergence of logistic regression |

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 )

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