pedtools: ped_complex – R documentation

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ped_complex

Complex pedigree structures

Description

Functions for creating a selection of pedigrees that are awkward to construct from scratch, or by using 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)

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.

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.

Value

A ped object.

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.

pedtools

Creating and Working with Pedigrees and Marker Data

v0.9.7

GPL-3

Authors

Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)

Initial release