prepPed: Prepares a pedigree by sorting and adding 'founders'

In matthewwolak/nadiv: (Non)Additive Genetic Relatedness Matrices

Prepares a pedigree by sorting and adding 'founders'

Description

This function takes a pedigree, adds missing founders, and then sorts the pedigree.

Usage

prepPed(pedigree, gender = NULL, check = TRUE)

Arguments

pedigree	An object, where the first 3 columns correspond to: ID, Dam, & Sire. See details.
gender	An optional character for the name of the column in pedigree that corresponds to the gender/sex of individuals. If specified, prepPed will assign a gender to any founders it adds to the pedigree.
check	A logical argument indicating if checks on the validity of the pedigree structure should be made

Details

Many functions (both in nadiv and from other programs) dealing with pedigrees must first sort a pedigree such that individuals appear in the ID column in rows preceding where they appear in either the Dam or Sire column. Further, these functions and programs require that all individuals in the dam and sire columns of a pedigree also have an entry in the ID column. This function easily prepares data sets to accommodate these requirements using a very fast topological sorting algorithm.

NOTE: more columns than just a pedigree can be passed in the pedigree argument. In the case of missing founders, these columns are given NA values for all rows where founders have been added to the pedigree. The entire object supplied to pedigree is ordered, ensuring that all information remains connected to the individual

Missing parents (e.g., base population) should be denoted by either 'NA', '0', or '*'.

When a non-null argument is given to gender, dams without an entry in the ID column (that are subsequently added to the pedigree) are given the gender designated for other dams (and similarly for sires).

The check argument performs checks on the format of the pedigree supplied to try and identify any issues regarding the notation of missing values and validity of the basic pedigree for further processing.

Value

The pedigree object (can have more columns than just ID, Dam, and Sire), where: (1) the ID column contains an ID for all individuals from the original pedigree object's ID, Dam, and Sire columns (i.e., founders are added) and (2) the pedigree is now sorted so that individuals are not in rows preceding either their Dam or Sire.

See Also

genAssign, prunePed

Examples

# First create an unordered pedigree with (4) missing founders
  warcolak_unsuitable <- warcolak[sample(seq(5, nrow(warcolak), 1),
	size = (nrow(warcolak) - 4), replace = FALSE), ]
  nrow(warcolak)
  nrow(warcolak_unsuitable)
# Fix and sort the pedigree
## Automatically assign the correct gender to the added founders
### Also sort the data accompanying each individual
  warcolak_fixed_ordered <- prepPed(warcolak_unsuitable, gender = "sex")
  head(warcolak_fixed_ordered)

matthewwolak/nadiv documentation built on July 7, 2023, 1:24 p.m.