ped_complex: Complex pedigree structures

In pedtools: Creating and Working with Pedigrees and Marker Data

Complex pedigree structures

Description

Functions for creating a selection of pedigrees that are awkward to construct from scratch or with the simple structures described in ped_basic.

Usage

doubleCousins(
  degree1,
  degree2,
  removal1 = 0,
  removal2 = 0,
  half1 = FALSE,
  half2 = FALSE,
  child = FALSE
)

doubleFirstCousins()

quadHalfFirstCousins()

fullSibMating(n)

halfSibStack(n)

halfSibTriangle(g)

Arguments

degree1, degree2, removal1, removal2	Nonnegative integers.
half1, half2	Logicals, indicating if the fathers (resp. mothers) should be full or half cousins.
child	A logical: Should a child be added to the double cousins?
n	A positive integer indicating the number of crossings.
g	A positive integer; the number of generations.

Details

The function doubleCousins returns a pedigree linking two individuals who are simultaneous paternal and maternal cousins. More precisely, they are:

• paternal (full or half) cousins of type (degree1, removal1)

• maternal (full or half) cousins of type (degree2, removal2).

For convenience, a wrapper doubleFirstCousins is provided for the most common case, double first cousins.

quadHalfFirstCousins produces a pedigree with quadruple half first cousins.

fullSibMating crosses full sibs consecutively n times.

halfSibStack produces a breeding scheme where the two individuals in the final generation are simultaneous half k'th cousins, for each ⁠k = 0,...,n-1⁠.

halfSibTriangle produces a triangular pedigree in which every pair of parents are half siblings.

Value

A ped object.

See Also

ped_basic

Examples

# Consecutive brother-sister matings.
x = fullSibMating(2)
# plot(x)

# Simultaneous half siblings and half first cousins
x = halfSibStack(2)
# plot(x)

# Double first cousins
x = doubleFirstCousins()
# plot(x)

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

# Triangular half-sib pattern
x = halfSibTriangle(4)
# plot(x)

pedtools documentation built on Nov. 5, 2023, 5:06 p.m.