getGenotypes: Genotype matrix

In pedtools: Creating and Working with Pedigrees and Marker Data

Genotype matrix

Description

Extract the genotypes of multiple individuals/markers in form of a matrix.

Usage

getGenotypes(x, ids = NULL, markers = NULL, sep = "/", missing = "-")

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.
sep	A single string to be used as allele separator in marker genotypes.
missing	A single string to be used for missing alleles.

Value

getGenotypes() returns a character matrix with length(ids) rows and length(markers) columns.

See Also

getAlleles()

Examples

x = nuclearPed(1)
m1 = marker(x, `2` = "1/2", alleles = 1:2, name = "m1")
m2 = marker(x, `3` = "2/2", alleles = 1:2, name = "m2")
x = setMarkers(x, list(m1, m2))

getGenotypes(x)


### A list of pedigrees

s = transferMarkers(x, singleton("s"))
peds = list(x, s)

getGenotypes(peds)

pedtools documentation built on Nov. 5, 2023, 5:06 p.m.