ped_modify: Add/remove pedigree members

In magnusdv/pedtools: Creating and Working with Pedigrees and Marker Data

Add/remove pedigree members

Description

Functions for adding or removing individuals in a 'ped' object.

Usage

addChildren(
  x,
  father = NULL,
  mother = NULL,
  nch = NULL,
  sex = 1L,
  ids = NULL,
  verbose = TRUE
)

addChild(x, parents, id = NULL, sex = 1, verbose = TRUE)

addSon(x, parents, id = NULL, verbose = TRUE)

addDaughter(x, parents, id = NULL, verbose = TRUE)

addParents(x, id, father = NULL, mother = NULL, verbose = TRUE)

removeIndividuals(
  x,
  ids,
  remove = c("descendants", "ancestors"),
  returnLabs = FALSE,
  verbose = TRUE
)

branch(x, id)

## S3 method for class 'ped'
subset(x, subset, ...)

Arguments

x	A ped object, or a list of such.
father, mother	Single ID labels. At least one of these must be an existing member of x. The other may be (i) another existing member, (ii) a new founder to be created, or (iii) missing (i.e., NULL), in which case the other parent is created and given a suitable name.
nch	A positive integer indicating the number of children to be created. Default: 1.
sex	Gender codes of the created children (recycled if needed).
ids	A vector of ID labels. In addChildren() these are the children to be created. If NULL (default) given, automatic labels are generated.
verbose	A logical: Verbose output or not.
parents	A vector of 1 or 2 ID labels, of which at least one must be an existing member of x.
id	The ID label of a pedigree member.
remove	Either "ancestors" or "descendants" (default), dictating the method of removing pedigree members. Abbreviations are allowed.
returnLabs	A logical, by default FALSE. If TRUE, removeIndividuals() returns only the labels of all members to be removed, instead of actually removing them.
subset	A character vector (or coercible to such) with ID labels forming a connected sub-pedigree.
...	Not used.

Details

In addChildren() and addParents(), labels of added individuals are generated automatically if they are not specified by the user. The automatic labelling uses the smallest integers not already in use.

addChild(), addSon() and addDaughter() are convenient wrappers for the most common use of addChildren(), namely adding a single child to a pedigree. Note that the parents can be given in any order. If only one parent is supplied, the other is created as a new individual.

removeIndividuals() removes the individuals indicated with ids along with all of their ancestors OR descendants, depending on the remove argument. Leftover spouses disconnected to the remaining pedigree are also removed. An error is raised if result is a disconnected pedigree.

The branch() function extracts the sub-pedigree formed by id and all his/her spouses and descendants.

Finally, subset() can be used to extract any connected sub-pedigree. (Note that in the current implementation, the function does not actually check that the indicated subset forms a connected pedigree; failing to comply with this may lead to obscure errors.)

Value

The modified ped object.

See Also

ped(), relabel(), swapSex()

Examples

x = nuclearPed(1) |>
  addSon(3) |>
  addParents(4, father = 6, mother = 7) |>
  addChildren(father = 6, mother = 7, nch = 3, sex = c(2,1,2))

# Remove 6 and 7 and their descendants
y1 = removeIndividuals(x, 6:7)

# Remove 8-10 and their parents
y2 = removeIndividuals(x, 8:10, remove = "ancestors")

# Adding a child across components
z = singletons(1:2, sex = 1:2) |> addDaughter(1:2)

magnusdv/pedtools documentation built on April 25, 2024, 4:25 a.m.