Compute Parent Adjacency Matrix with Multiple Approaches

Usage

compute_parent_adjacency(
  ped,
  component,
  adjacency_method = "indexed",
  saveable,
  resume,
  save_path,
  verbose,
  lastComputed,
  nr,
  checkpoint_files,
  update_rate,
  parList,
  lens,
  save_rate_parlist,
  ...
)

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" or "indexed"
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
nr: the number of rows in the pedigree dataset
checkpoint_files: a list of checkpoint files
update_rate: numeric. The rate at which to print 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
...: 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.