Compute Parent Adjacency Matrix with Multiple Approaches

Usage

computeParentAdjacency(
  ped,
  component,
  adjacency_method = "direct",
  saveable,
  resume,
  save_path,
  verbose = FALSE,
  lastComputed = 0,
  checkpoint_files,
  update_rate,
  parList,
  lens,
  save_rate_parlist,
  adjBeta_method = NULL,
  config,
  compress = config$compress,
  ...
)

Arguments

ped: a pedigree dataset. Needs ID, momID, and dadID columns
component: character. Which component of the pedigree to return. See Details.
adjacency_method: character. The method to use for computing the adjacency matrix. Options are "loop", "indexed", direct or beta
saveable: logical. If TRUE, save the intermediate results to disk
resume: logical. If TRUE, resume from a checkpoint
save_path: character. The path to save the checkpoint files
verbose: logical. If TRUE, print progress through stages of algorithm
lastComputed: the last computed index
checkpoint_files: a list of checkpoint files
update_rate: the rate at which to update the progress
parList: a list of parent-child relationships
lens: a vector of the lengths of the parent-child relationships
save_rate_parlist: numeric. The rate at which to save the intermediate results by parent list. If NULL, defaults to save_rate*1000
adjBeta_method: numeric The method to use for computing the building the adjacency_method matrix when using the "beta" build
config: a configuration list that passes parameters to the function
compress: logical. If TRUE, use compression when saving the checkpoint files. Defaults to TRUE.
...: 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.