as.matrix.ped: Convert 'ped' to matrix

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

Convert ped to matrix

Description

Converts a ped object to a numeric matrix using internal labels, with additional info necessary to recreate the original ped attached as attributes.

Usage

## S3 method for class 'ped'
as.matrix(x, include.attrs = TRUE, ...)

restorePed(x, attrs = NULL, validate = TRUE)

Arguments

x	a ped object. In restorePed: A numerical matrix.
include.attrs	a logical indicating if marker annotations and other info should be attached as attributes. See Value.
...	not used.
attrs	a list containing labels and other ped info compatible with x, in the format produced by as.matrix. If NULL, the attributes of x itself are used.
validate	a logical, forwarded to ped(). If FALSE, no checks for pedigree errors are performed.

Details

restorePed is the reverse of as.matrix.ped.

Value

For as.matrix: A numerical matrix with pedsize(x) rows. If include.attrs = TRUE the following attributes are added to the matrix, allowing x to be exactly reproduced by restorePed:

• FAMID the family identifier (a string)

• LABELS the ID labels (a character vector)

• UNBROKEN_LOOPS a logical indicating whether x has unbroken loops

• LOOP_BREAKERS a numerical matrix, or NULL

• markerattr a list of length nMarkers(x), containing the attributes of each marker

For restorePed: A ped object.

Author(s)

Magnus Dehli Vigeland

See Also

ped()

Examples

x = relabel(nuclearPed(1), letters[1:3])

# To examplify the ped -> matrix -> ped trick, we show how to
# reverse the internal ordering of the pedigree.
m = as.matrix(x, include.attrs = TRUE)
m[] = m[3:1, ]

# Must reverse the labels also:
attrs = attributes(m)
attrs$LABELS = rev(attrs$LABELS)

# Restore ped:
y = restorePed(m, attrs = attrs)

# Of course a simpler way is use reorderPed():
z = reorderPed(x, 3:1)
stopifnot(identical(y, z))

magnusdv/pedtools documentation built on April 29, 2024, 10:34 p.m.