getGenotypes: Genotype matrix

In pedtools: Creating and Working with Pedigrees and Marker Data

Genotype matrix

Description

Extract the genotypes of specified individuals and markers from a pedigree object, and return them as a character matrix.

Usage

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

Arguments

x	A ped object or a list of such.
ids	A vector of ID labels, or a function operating on x, e.g., typedMembers(). By default (ids = NULL) all individuals are included, also non-genotyped ones.
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.
Xchrom	A single logical, or NULL (default). May be used to indicate if all (or none) markers are on X, if this is known in advance.

Value

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

See Also

getAlleles()

Examples

x = nuclearPed() |>
  addMarker(`2` = "1/2", name = "m1") |>
  addMarker(`3` = "a/a", name = "m2")

getGenotypes(x)

### A list of pedigrees

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

getGenotypes(peds)

# Using a function to select individuals
getGenotypes(x, ids = typedMembers)

pedtools documentation built on Nov. 5, 2025, 5:50 p.m.