Imputes the variants in a specified group, conditional on other variants, based on the recombination model. This is intented for use a subroutine of the conditional randomization test.
impute_variant_fast(x, p1, p2, group, d, fb_result = NULL, lambda = 0.012, epsilon = 1e-08, window_size = 200)
| x | 0-1 vector of length p. The observed haplotypes of the offspring. |
|---|---|
| p1 | 0-1 vector of length p. One of the parental haplotypes
giving rise to |
| p2 | 0-1 vector of length p. The other parental haplotypes
giving rise to |
| group | a subset of indices of 1:p. This subset of variants will be imputed. |
| d | numeric vector of length p. The genetic distance between variants |
| lambda | the recombination rate, in units of the vector d |
| epsilon | the pointwise mutation rate |
| window_size | when imputing the variants, look only at a window of this size surrounding the group g. A smaller window size leads to faster computation and avoids numerical issues. |
A vector of the same length as group containing the imputed variants.