geneDrop: Functions to conduct gene dropping through a pedigree

In nadiv: (Non)Additive Genetic Relatedness Matrices

Functions to conduct gene dropping through a pedigree

Description

Functions that perform and summarize gene dropping conducted on supplied pedigrees

Usage

geneDrop(
  pedigree,
  N,
  parallel = FALSE,
  ncores = getOption("mc.cores", 2L),
  ...
)

## Default S3 method:
geneDrop(
  pedigree,
  N,
  parallel = FALSE,
  ncores = getOption("mc.cores", 2L),
  ...
)

## S3 method for class 'numPed'
geneDrop(
  pedigree,
  N,
  parallel = FALSE,
  ncores = getOption("mc.cores", 2L),
  ...
)

Arguments

pedigree	A pedigree with columns organized: ID, Dam, Sire.
N	The number of times to iteratively trace alleles through the pedigree
parallel	A logical indicating whether or not to use parallel processing. Note, this may only be available for Mac and Linux operating systems.
ncores	The number of cpus to use when constructing the dominance relatedness matrix. Default is all available.
...	Other arguments that can be supplied to alter what summaries are reported.

Details

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

parallel = TRUE should only be used on Linux or Mac operating systems (i.e., not Windows).

Founder allelic values (the alleles assigned to an individual's maternal, paternal, or both haplotypes when the maternal, paternal, or both parents are missing) are equivalent positive and negative integer values corresponding to the maternal and paternal haplotypes, respectively. For example, if the first individual in the pedigree has two unknown parents it will have the following two allelic values: 1=maternal haplotype and -1=paternal haplotype.

Value

a list:

IDs

Original identities in the pedigree

maternal

Simulated maternal haplotypes

paternal

Simulated paternal haplotypes

numericPedigree

Pedigree in class numPed for convenient post-processing of haplotypes

Author(s)

[e-mail]

See Also

makeDsim

Examples

  geneDrop(Mrode2, N = 10)

nadiv documentation built on Dec. 8, 2022, 1:11 a.m.