ped2add: Take a pedigree and turn it into an additive genetics...

In R-Computing-Lab/BGMisc: An R Package for Extended Behavior Genetics Analysis

Take a pedigree and turn it into an additive genetics relatedness matrix

Description

Take a pedigree and turn it into an additive genetics relatedness matrix

Usage

ped2add(
  ped,
  max.gen = 25,
  sparse = FALSE,
  verbose = FALSE,
  gc = FALSE,
  flatten.diag = FALSE,
  standardize.colnames = TRUE,
  transpose_method = "tcrossprod",
  adjacency_method = "direct",
  saveable = FALSE,
  resume = FALSE,
  save_rate = 5,
  save_rate_gen = save_rate,
  save_rate_parlist = 1000 * save_rate,
  save_path = "checkpoint/",
  ...
)

Arguments

ped	a pedigree dataset. Needs ID, momID, and dadID columns
max.gen	the maximum number of generations to compute (e.g., only up to 4th degree relatives). The default is 25. However it can be set to infinity. 'Inf' uses as many generations as there are in the data.
sparse	logical. If TRUE, use and return sparse matrices from Matrix package
verbose	logical. If TRUE, print progress through stages of algorithm
gc	logical. If TRUE, do frequent garbage collection via gc to save memory
flatten.diag	logical. If TRUE, overwrite the diagonal of the final relatedness matrix with ones
standardize.colnames	logical. If TRUE, standardize the column names of the pedigree dataset
transpose_method	character. The method to use for computing the transpose. Options are "tcrossprod", "crossprod", or "star"
adjacency_method	character. The method to use for computing the adjacency matrix. Options are "loop" or "indexed"
saveable	logical. If TRUE, save the intermediate results to disk
resume	logical. If TRUE, resume from a checkpoint
save_rate	numeric. The rate at which to save the intermediate results
save_rate_gen	numeric. The rate at which to save the intermediate results by generation. If NULL, defaults to save_rate
save_rate_parlist	numeric. The rate at which to save the intermediate results by parent list. If NULL, defaults to save_rate*1000
save_path	character. The path to save the checkpoint files
...	additional arguments to be passed to ped2com

Details

The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions". For more advanced scenarios and detailed explanations, consult this vignette.

R-Computing-Lab/BGMisc documentation built on April 3, 2025, 3:12 p.m.