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

Usage

ped2add(
  ped,
  max_gen = 25,
  sparse = TRUE,
  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 = 1e+05 * save_rate,
  save_path = "checkpoint/",
  compress = TRUE,
  mz_twins = FALSE,
  mz_method = "addtwins",
  ...
)

Arguments

ped: a pedigree dataset. Needs ID, momID, and dadID columns
max_gen: the maximum number of iterations that the adjacency matrix is multiplied to get the relatedness matrix. `Inf` uses as many iterations as there are in the data. Defaults to 25.
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", "indexed", direct or beta
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
compress: logical. If TRUE, use compression when saving the checkpoint files. Defaults to TRUE.
mz_twins: logical. If TRUE, merge MZ co-twin columns in the r2 matrix before tcrossprod so that MZ twins are coded with relatedness 1 instead of 0.5. Twin pairs are identified from the twinID column. When a zygosity column is also present, only pairs where both members have zygosity == "MZ" are used; otherwise all twinID pairs are assumed to be MZ. Defaults to FALSE.
mz_method: character. The method to handle MZ twins. Options are "merging" (default) or "addtwins". "addtwins" adds the twin2 column to the twin1 column before tcrossprod so that all relatedness flows through a single source, then leaves the twin2 column as zero and relies on the fact that the row/col names are the same to copy the values back to twin2 after tcrossprod. "merging" merges the twin2 column into the twin1 column before tcrossprod and then copies the values back to twin2 after tcrossprod so that both twins appear in the final matrix.
...: 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.