realised {ibdsim2}

Realised relatedness

Description

Compute the realised values of various pedigree coefficients, from simulated data. The current implementation covers inbreeding coefficients for single pedigree members, and kinship, kappa and condensed identity coefficients for pairwise relationships.

Usage

realisedInbreeding(sims, id = NULL, unit = "cm")

realisedKinship(sims, ids = NULL, unit = "cm")

realisedKappa(sims, ids = NULL, unit = "cm")

realisedIdentity(sims, ids = NULL, unit = "cm")

Arguments

sims

A list of genome simulations, as output by ibdsim().

id, ids

A vector with one or two ID labels.

unit

Either "mb" (megabases) or "cm" (centiMorgan); the length unit for genomic segments. Default is "cm", which normally gives lower variance.

Details

The inbreeding coefficient f of a pedigree member is defined as the probability of autozygosity (homozygous for alleles that are identical by descent) in a random autosomal locus. Equivalently, the inbreeding coefficient is the expected autozygous proportion of the autosomal chromosomes.

The realised inbreeding coefficient f_R in a given individual is the actual fraction of the autosomes covered by autozygous segments. Because of the stochastic nature of meiotic recombination, this may deviate substantially from the pedigree-based expectation.

Similarly, the pedigree-based IBD coefficients \kappa_0, \kappa_1, \kappa_2 of noninbred pairs of individuals have realised counterparts. For any given pair of individuals we define k_i to be the actual fraction of the autosome where the individuals share exactly i alleles IBD, where i = 0,1,2.

Finally, we can do the same thing for each of the nine condensed identity coefficients of Jacquard. For each i = 1,...,9 we define D_i the be the fraction of the autosome where a given pair of individuals are in identity state i. This uses the conventional ordering of the nine condensed identity states; see for instance the ribd GitHub page.

Examples

# Realised IBD coefficients between full siblings
x = nuclearPed(2)
s = ibdsim(x, N = 2) # increase N
realisedKappa(s, ids = 3:4)

###########

# Realised inbreeding coefficients, child of first cousins
x = cousinPed(1, child = TRUE)
s = ibdsim(x, N = 2) # increase N
realisedInbreeding(s, id = 9)

# Same data: realised kinship coefficients between the parents
realisedKinship(s, ids = parents(x, 9))

###########

# Realised identity coefficients after full sib mating
x = fullSibMating(1)
s = ibdsim(x, N = 2) # increase N
realisedIdentity(s, ids = 5:6)