build_pedigree: Build pedigree

In famuvie/breedR: Statistical Methods for Forest Genetic Resources Analysts

Build pedigree

Description

Builds a full pedigree out of observed data with sorting and recoding.

Usage

build_pedigree(x, self = x[[1]], sire = x[[2]], dam = x[[3]], data)

## S3 method for class 'pedigree'
as.data.frame(x, ...)

Arguments

x	if given, a vector of length 3 with indices or names of columns in data corresponding to self, sire and dam codes
self	index or column name in data with codes of sires
sire	index or column name in data with codes of individuals
dam	index or column name in data with codes of dams
data	a dataframe or a list to take the individual codes from
...	Not used

Details

A full pedigree requires that all the individual codes for sires or dams are present as individuals themselves, possibly with unknown parents. Therefore, for using it in a statistical model, it is necessary to complete the pedigree by introducing new individuals with unknown parents.

Furthermore, the codes must be sorted in ascending and consecutive order beginning from 1, and the offspring must follow parents. All this is checked, and the pedigree is reordered and recoded if needed.

If recoding is needed, the function issues a warning and an attribute 'map' is attached to the pedigree, such that map[i] = j means that code i was renumbered as j. Therefore, if x is a vector with original codes, map[x] gives the new codes. Conversely, match(y, map) back-transforms to original codes.

Value

A well-formed 'pedigree'-class object. Possibly sorted and recoded.

Functions

• as.data.frame(pedigree): Coerce to a data.frame. One row per individual, the first column being the identification code, and the other two columns are dad and mum codes respectively.

See Also

check_pedigree

Examples

# Founders are missing in the globulus dataset
data(globulus)
check_pedigree(globulus[,c('self', 'dad', 'mum')])
# build_pedigree completes the missing information
ped <- build_pedigree(c('self', 'dad', 'mum'), data = globulus)
check_pedigree(ped)

famuvie/breedR documentation built on Aug. 6, 2024, 9:10 p.m.