ibdsegments (version 1.0.1)

total_ibd_dist_moments: Compute moments of probability distribution of total IBD

Description

The total_ibd_dist_moments function computes mean and variance of the probability distribution of the total IBD length (or fraction) over one autosome. The function uses double numerical integration.

Usage

total_ibd_dist_moments(
  pedigree,
  ids = pedtools::leaves(pedigree),
  fraction = FALSE,
  states = "ibd",
  ibd_state = 1L,
  chromosome_length = 267.77
)

Value

list

Arguments

pedigree

Pedigree in pedtools::ped form.

ids

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

fraction

If TRUE, the distribution of the IBD fraction instead of length will be returned. Default is FALSE.

states

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

ibd_state

Default is 1.

chromosome_length

Default is 267.77 cM (an estimate of the length of chromosome 1).

Examples

# Full Siblings are double IBD with 25% probability
# we may compute the expectation and variance of the total length of
# a chromosome that is double IBD for a chromosome of 100 cM (i.e. 1 Morgan)
m <- total_ibd_dist_moments(pedigree = pedtools::nuclearPed(nch = 2),
                       ibd_state = 2, chromosome_length = 100)
m

# compare to numerical integration of the full distribution
d_fs <- total_ibd_dist(pedigree = pedtools::nuclearPed(nch = 2),
ibd_state = 2, chromosome_length = 100)

m2 <- list(mean = E(d_fs), variance = var(d_fs), sd = sd(d_fs))
m2

stopifnot(all.equal(m, m2))

# Expectation and variance of _fraction_ of the genome that is
# double IBD between four full siblings
m4 <- total_ibd_dist_moments(pedigree = pedtools::nuclearPed(nch = 4),
ibd_state = 2, chromosome_length = 100, fraction = TRUE)
m4

stopifnot(all.equal(0.25^3, m4$mean))