pairwise_kin_logl_ratios: compute pairwise log likelihood ratios between two sets of...

In eriqande/CKMRsim: Inference of Pairwise Relationships Using Likelihood Ratios

compute pairwise log likelihood ratios between two sets of individuals

Description

This computes log likelihoods for all pairs formed by comparing every individual in D1 to every individual in D2. If D1 and D2 are different objects, it is assumed that they include disjoint groups of individuals, and all pairs are returned. If D1 and D2 are the same object, then the output is filtered so that each pairwise comparison appears only once, and so that the comparisons between the same individual are dropped.

Usage

pairwise_kin_logl_ratios(
  D1,
  D2,
  CK,
  numer,
  denom = NULL,
  keep_top = NULL,
  num_cores = parallel::detectCores()
)

Arguments

D1	long format genotype data frame of the first set of individuals. If doing parent-offspring, this should be the parents.
D2	long format genotype data frame of the second set of individuals. If doing parent-offspring, this should be the offspring.
CK	the ckmr object created previously from the data that D1 and D2 came from.
numer	the relationship that should be the numerator of the logl ratio. This relationship must appear in the ckmr object CK.
denom	the relationship that should be the denominator of the logl ratio. This relationship must appear in the ckmr object CK. Leave empty to only calculate the log likelihood of of the numerator.
keep_top	If this is given as an integer, then for each individual in D2, only the keep_top individuals with the highest logl ratios are retained for the result. The rest are discarded.
num_cores	The number of cores to use with mclapply. This is ignored if using windows (in which case it is always set to one.) Otherwise, by default it uses all the cores available.

eriqande/CKMRsim documentation built on Aug. 2, 2024, 7:23 a.m.