R/crt_helpers.r
get_fb_results.RdReturns the result of the forward backward algorithm for a sepcified group.
Intended for use as a pre-computation step for the linear_crt function.
get_fb_results(H, H_parent, anc, group, d, lambda = 0.012, epsilon = 1e-08, window_size = 200)
| H | an (n x p) matrix of the subject haplotypes |
|---|---|
| H_parent | and (n_2 x p) matrix of the parental haplotypes |
| anc | a (n x 2) table of ancestries. anc[i, 1] and and[i, 2] give the rows of H_parent corresponding to the parents of subject i |
| group | a list of of indices of the group to test. Should be a continuous region, such as 10:20. |
| d | a vector of length p giving the genetic distances between sites |
| lambda | the recombination rate, in units of d |
| epsilon | the pointwise mutation rate |
| window_size | the number of sites to on each size of the group to use when computing the forward-backward probabilities. Smaller groups improve speed and avoid numerical issues. |
a (n x 3) matrix giving the results of the forward-backward algorithm.
See the documentation of the forward_backward_ function for output information.