ribd (version 1.7.1)

inbreeding: Inbreeding coefficients

Description

Compute the inbreeding coefficients of all members of a pedigree. Both autosomal and X-chromosomal coefficients are supported. This function is a simple wrapper of kinship(). Note that pedigree founders are allowed to be inbred; see pedtools::founderInbreeding() for how to set this up, and see Examples below.

Usage

inbreeding(x, ids = NULL, Xchrom = FALSE)

Value

If ids has length 1, the inbreeding coefficient of this individual is returned as a single unnamed number.

Otherwise, the output is a named numeric vector containing the inbreeding coefficients of the indicated pedigree members (if ids = NULL: all).

Arguments

x

A pedigree in the form of a ped object, or a list of such.

ids

A vector of ID labels, or NULL (default).

Xchrom

A logical, indicating if the autosomal (default) or X-chromosomal inbreeding coefficients should be computed.

Details

The autosomal inbreeding coefficient of a pedigree member is defined as the probability that, at a random autosomal locus, the two alleles carried by the member are identical by descent relative to the pedigree. It follows from the definition that the inbreeding coefficient of a non-founder equals the kinship coefficient of the parents.

The implementation here uses kinship() to compute the kinship matrix, and computes the inbreeding coefficients from the diagonal, by the formula $$f_a = 2*\phi_{aa} - 1.$$

The X chromosomal inbreeding coefficient of females are defined (and computed) similarly to the autosomal case above. For males is it always defined as 1.

See Also

kinship()

Examples

# Child of half siblings: f = 1/8
x = halfCousinPed(0, child = TRUE)

# Inbreeding vector
inbreeding(x)

# Simpler output using the `ids` argument:
inbreeding(x, ids = 6)


### X-chromosomal inbreeding ###

# Males have inbreeding coefficient 1
stopifnot(inbreeding(x, ids = 6, Xchrom = TRUE) == 1)

y1 = swapSex(x, ids = 6)  # female child
stopifnot(inbreeding(y1, ids = 6, Xchrom = TRUE) == 0)

y2 = swapSex(y1, ids = 2) # female ancestor
stopifnot(inbreeding(y2, ids = 6, Xchrom = TRUE) == 0.25)


### Inbred founder ###

# Mother 100% inbred
founderInbreeding(x, ids = 2) = 1

inbreeding(x)


# Example with selfing and complete inbreeding
s = selfingPed(1)
founderInbreeding(s, 1) = 1
stopifnot(inbreeding(s, ids = 2) == 1)