Construct Adjacency Matrix for Parent-Child Relationships Using Direct Method

This function constructs an adjacency matrix for parent-child relationships using a direct method. It identifies parent-child pairs based on the specified component of relatedness.

Usage

.adjDirect(
  ped,
  component,
  saveable,
  resume,
  save_path,
  verbose,
  lastComputed,
  checkpoint_files,
  update_rate,
  parList,
  lens,
  save_rate_parlist,
  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.

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

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

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