ped_modify {pedtools} | R Documentation |
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 |
father , mother |
Single ID labels. At least one of these must be an
existing member of |
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 |
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 |
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, |
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
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)