relabel: Get or modify pedigree labels

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

Get or modify pedigree labels

Description

Functions for getting or changing the ID labels of pedigree members.

Usage

relabel(
  x,
  new = "asPlot",
  old = labels(x),
  reorder = FALSE,
  returnLabs = FALSE,
  .alignment = NULL
)

## S3 method for class 'ped'
labels(object, ...)

## S3 method for class 'list'
labels(object, ..., unlist = TRUE)

Arguments

x	A ped object or a list of such.
new	The following values are valid (see Details and Examples): a character vector containing new labels. If named, interpreted as old = new a function, which should take the old labels as input and output a character of the same length one of the special keywords "asPlot" (default) or "generations"
old	A vector of ID labels, of the same length as new. (Ignored if new is one of the special words.) If not given, taken from the names of new if these exist.
reorder	A logical. If TRUE, reorderPed() is called on x after relabelling. Default: FALSE.
returnLabs	A logical. If TRUE, the new labels are returned as a named character vector.
.alignment	A list of alignment details for x, used if new equals "asPlot" or "generations". If not supplied, this is computed internally with .pedAlignment().
object	A ped object.
...	Not used.
unlist	A logical; if TRUE (default), the output is unlisted to a single character vector.

Details

By default, relabel(x) relabels everyone as 1, 2, ..., in the order given by the plot (top to bottom; left to right).

Alternatively, relabel(x, "generations") labels the members in the top generation I-1, I-2, ..., in the second generation II-1, II-2, ..., etc.

Value

• labels() returns a character vector containing the ID labels of all pedigree members. If the input is a list of ped objects, the output is a list of character vectors.

• relabel() by default returns a ped object similar to x, but with modified labels. If returnLabs is TRUE, the new labels are returned as a named character vector

See Also

ped()

Examples

x = nuclearPed()
x
labels(x)

y = relabel(x, new = "girl", old = 3)
y

# Back to the numeric labels
z = relabel(y)
stopifnot(identical(x,z))

# Generation labels
relabel(x, "generations")

magnusdv/pedtools documentation built on April 9, 2024, 7:35 a.m.