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Take a pedigree and turn it into a relatedness matrix

Usage

ped2com(
  ped,
  component,
  max.gen = 25,
  sparse = FALSE,
  verbose = FALSE,
  gc = FALSE,
  flatten.diag = FALSE,
  standardize.colnames = TRUE,
  transpose_method = "tcrossprod",
  adjacency_method = "indexed",
  saveable = FALSE,
  resume = FALSE,
  save_rate = 5,
  save_rate_gen = save_rate,
  save_rate_parlist = 1e+05 * save_rate,
  update_rate = 100,
  save_path = "checkpoint/",
  ...
)

Arguments

ped

a pedigree dataset. Needs ID, momID, and dadID columns

component

character. Which component of the pedigree to return. See Details.

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

update_rate

numeric. The rate at which to print progress

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.