get_fb_results: Forward-backward algorithm for parent-offspring trio of...
In stephenbates19/digitaltwins: Causal inference for SNPs

Returns the result of the forward backward algorithm for a sepcified group. Intended for use as a pre-computation step for the linear_crt function.

1 2	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.

stephenbates19/digitaltwins documentation built on Feb. 25, 2020, 12:41 a.m.