pedtools: as.matrix.ped – R documentation

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as.matrix.ped

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

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))

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