d_ibd {ibdsegments} | R Documentation |
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
)
Arguments
ibd |
Integer vector. Taking values 0, 1, 2 for |
pedigree |
Pedigree in |
ids |
Ids for which IBD is observed. Defaults to |
recombination_rate_by_locus |
Numeric vector with length one shorter than |
states |
One of |
log10 |
Should the log10 likelihood be returned? Default is |
Value
Numeric
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")
[Package ibdsegments version 1.0.1 Index]