pedCreate: Create simple pedigrees

In paramlink: Parametric Linkage and Other Pedigree Analysis in R

Create simple pedigrees

Description

These are utility functions for creating some common pedigree structures as linkdat objects.

Usage

nuclearPed(noffs, sex)

cousinsPed(degree, removal = 0, degree2 = NULL, child = FALSE)

halfCousinsPed(degree, removal = 0, degree2 = NULL, child = FALSE)

doubleCousins(degree1, degree2, removal1 = 0, removal2 = 0, child = FALSE)

doubleFirstCousins()

quadHalfFirstCousins()

fullSibMating(generations)

halfSibStack(generations)

cousinPed(degree)

halfCousinPed(degree)

Arguments

noffs	A positive integer, the number of offspring in the nuclear family.
sex	A vector of length noffs; indicating the genders (1=male, 2=female) of the offspring. If missing, all offspring are taken to be males.
degree, degree1, degree2	Non-negative integers, indicating the degree of cousin-like relationships: 0=siblings, 1=first cousins; 2=second cousins, a.s.o. See Details and Examples.
removal, removal1, removal2	Non-negative integers, indicating removals of cousin-like relationships. See Details and Examples.
child	A logical: Should an inbred child be added to the two cousins?
generations	A positive integer indicating the number of crossings.

Details

All individuals are created as unaffected. Use swapAff to edit this (see Examples). Use swapSex to change gender of pedigree members.

The call cousinsPed(degree=n, removal=k) creates a pedigree with two n'th cousins, k times removed. By default, removals are added on the right side. To override this, the parameter degree2 can be used to indicate explicitly the number of generations on the right side of the pedigree. When degree2 is given removal is ignored. (Similarly for halfCousinsPed.)

The function doubleCousins creates two individuals whose fathers are cousins (degree1, removal1) as well as their mothers (degree2, removal2). For simplicity, a wrapper doubleFirstCousins is provided for the most common case, double first cousins. Finally quadHalfFirstCousins produces a pedigree with quadruple half first cousins.

fullSibMating crosses full sibs continuously for the indicated number of generations.

halfSibStack produces a breeding scheme where the two individuals in the final generation are simultaneously half siblings and half n'th cousins, where n=1,...,generations.

cousinPed and halfCousinPed (written without the 's') are depreciated functions kept for backwards compatibility. They create cousin pedigrees, but without possibility for removals, and with a different ordering than their replacements cousinsPed and halfCousinsPed.

Value

A linkdat object.

See Also

swapAff, swapSex, removeIndividuals, addOffspring, relabel

Examples

# A nuclear family with 2 boys and 3 girls,
# where the father and the two boys are affected.
x = nuclearPed(noffs=5, sex=c(1,1,2,2,2))
x = swapAff(x, ids=c(1,3,4))

# Half sibs:
halfCousinsPed(degree=0)

# Grand aunt:
cousinsPed(degree=0, removal=2)

# Second cousins once removed.
cousinsPed(degree=2, removal=1)

# Again second cousins once removed,
# but with the 'removal' on the left side.
cousinsPed(degree=3, degree2=2)

# A child of first cousin parents.
cousinsPed(degree=1, child=TRUE)

# Consecutive brother-sister matings.
fullSibMating(3)

# Simultaneous half siblings and half first cousins
halfSibStack(2)

# Double first cousins
doubleFirstCousins()

# Quadruple half first cousins
# Weird plotting behaviour for this pedigree.
x = quadHalfFirstCousins()
#plot(x)

paramlink documentation built on April 15, 2022, 9:06 a.m.