ibdsegments (version 1.0.1)

d_ibd: Compute probability of IBD for pedigree members

Description

The d_ibd function computes the likelihood of IBD for one position or multiple linked markers on the same chromosome.

Usage

d_ibd(
  ibd,
  pedigree,
  ids = pedtools::leaves(pedigree),
  recombination_rate_by_locus = numeric(),
  states = "ibd",
  log10 = FALSE
)

Value

Numeric

Arguments

ibd

Integer vector. Taking values 0, 1, 2 for states = "ibd" or states = "kappa", 1, ..., 9 for states="identity" and 1, ..., 15 for states = "detailed".

pedigree

Pedigree in pedtools::ped form.

ids

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

recombination_rate_by_locus

Numeric vector with length one shorter than ibd.

states

One of "ibd" (default), "kappa", "identity" or "detailed".

log10

Should the log10 likelihood be returned? Default is FALSE.

Examples

# Compute kappa0, kappa1, kappa2 for full siblings
ped_fs <- pedtools::nuclearPed(nch = 2)

k0 <- d_ibd(ibd = 0, pedigree = ped_fs)
k1 <- d_ibd(ibd = 1, pedigree = ped_fs)
k2 <- d_ibd(ibd = 2, pedigree = ped_fs)
c(k0, k1, k2)

stopifnot(identical(c(k0, k1, k2), c(0.25, 0.5, 0.25)))

# Compute kappa00 for two tightly linked loci
d_ibd(c(0,0), pedigree = ped_fs,
       recombination_rate_by_locus = c(0.01))

# or 100 tightly linked loci
d_ibd(rep(0, 100), pedigree = ped_fs,
               recombination_rate_by_locus = c(rep(0.01, 99)))

# Jacquard's 9 condensed and 15 detailed identity coefficients
ped_fs_mating <- pedtools::fullSibMating(1)

sapply(1:9, d_ibd, pedigree = ped_fs_mating, states = "identity")
sapply(1:15, d_ibd, pedigree = ped_fs_mating, states = "detailed")