ibdsegments (version 1.0.1)

multi_ibd_patterns: Compute probabilities of minimal multi-id IBD patterns

Description

For two full siblings at one locus, it is well known that there are three distinct minimal IBD patterns with probabilities 0.25, 0.5 and 0.25. The ribd::multiPersonIBD function generalises the computation of these patterns and their probabilities to more than two ids The multi_ibd_patterns function further generalises the computation to patterns across multiple loci.

Usage

multi_ibd_patterns(
  pedigree,
  ids = pedtools::leaves(pedigree),
  recombination_rate_by_locus = numeric()
)

Value

DataFrame

Arguments

pedigree

Pedigree in pedtools::ped form.

ids

Ids for which IBD is observed. Defaults to pedtools::leaves(pedigree).

recombination_rate_by_locus

Optionally a numeric vector with recombination rates.

Examples

# Compute IBD patterns for two full siblings...
multi_ibd_patterns(pedtools::nuclearPed(nch = 2))

# ... and the generalisation to three siblings
multi_ibd_patterns(pedtools::nuclearPed(nch = 3))

# Two full siblings at two tightly linked loci
multi_ibd_patterns(pedtools::nuclearPed(nch = 2),
                   recombination_rate_by_locus = 0.01)