ibd: Calculation of Identity by descent (IBD).

In KinformR: Relationship-Informed Pedigree and Variant Scoring

Calculation of Identity by descent (IBD).

Description

Use the relationship informationfrom the pedigree to estimate of the amount of the genome they have inherited it from a common ancestor without recombination.

Usage

ibd(a, b, c, d, n, K, theoretical = TRUE)

Arguments

a	Count of affected individuals
b	Count of obligate carriers
c	Count of children of either affecteds or carriers, with no children of their own
d	Count of Trees of unaffected individuals - specifically, two sequential generations (i.e. a parent and their offspring)
n	Count of the number of second generation progeny in a given tree.
K	The estimate of penetrance rate.
theoretical	Boolean indicating if the calculation should be theoretical IBD calculation (using only d and k), or if the calculation should use the provided n value.

Details

Can do this for the total potential relatedness in a pedigree (theoretical=TRUE), or for the actual relatedness across collected samples (theoretical=FALSE). For the theoretical=TRUE case, in the unaffected trees, if we have a sample from the parent, then the offspring do not provide any additional information for a max IBD calculation. This means that K does not scale with n.

For theoretical=FALSE, sometimes we don’t have the healthy parent in an unaffected tree, and only have a child. In this case, the IBD contribution from the child is 1/4, and since they’re unaffected and therefore are a counter-filter, they would contribute 1-1/4 = 3/4 to the total relatedness. Either the parent is a non-obligate carrier, or is a non-carrier. The probability of the children depends on which of those is true, so we have the additional set of terms in the theoretical=FALSE logic.

Value

pi-hat value. The proportion of genome shared between individuals.

Examples

ibd <- ibd(3, 1, 5, 2, 1, 0.4576484)

KinformR documentation built on Feb. 17, 2026, 5:07 p.m.