inbreeding {ribd}

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)

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.

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).

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)