getAlleles: Allele matrix manipulation

Description

Functions for getting and setting the genotypes of multiple individuals/markers simultaneously

Usage

getAlleles(x, ids = NULL, markers = NULL)
setAlleles(x, ids = NULL, markers = NULL, alleles)

Value

getAlleles() returns a character matrix with length(ids) rows and 2 * length(markers) columns. The ID labels of x are used as rownames, while the columns are named <m1>.1, <m1>.2, ... where <m1> is the name of the first marker, a.s.o.

setAlleles() returns a ped object identical to x, except for the modified alleles. In particular, all locus attributes are unchanged.

Arguments

x: A ped object or a list of such
ids: A vector of ID labels. If NULL (default) all individuals are included.
markers: A vector of indices or names of markers attaches to x. If NULL (default) all markers are included.
alleles: A character of the same format and dimensions as the output of getAlleles(x, ids, markers), or an object which can be converted by as.matrix() into such a matrix. See Details.

Details

If the alleles argument of setAlleles() is not a matrix, it is recycled (if necessary), and converted into a matrix of the correct dimensions. For example, setting alleles = 0 gives a simple way of removing the genotypes of some or all individuals (while keeping the markers attached).

Examples

Run this code

# Setup: Pedigree with two markers
x = nuclearPed(1)
x = addMarker(x, `2` = "1/2", alleles = 1:2, name = "m1")
x = addMarker(x, `3` = "2/2", alleles = 1:2, name = "m2")

# Extract allele matrix
mat1 = getAlleles(x)
mat2 = getAlleles(x, ids = 2:3, markers = "m2")
stopifnot(identical(mat1[2:3, 3:4], mat2))

# Remove all genotypes
y = setAlleles(x, alleles = 0)
y

# Setting a single genotype
z = setAlleles(y, ids = "1", marker = "m2", alleles = 1:2)

# Alternative: In-place modification with `genotype()`
genotype(y, id = "1", marker = "m2") = "1/2"
stopifnot(identical(y,z))


### Manipulation of pedlist objects
s = transferMarkers(x, singleton("s"))
peds = list(x, s)

getAlleles(peds)

setAlleles(peds, ids = "s", marker = "m1", alleles = 1:2)