Take a pedigree and turn it into a mitochondrial relatedness matrix

Usage

ped2mit(
  ped,
  max.gen = 25,
  sparse = FALSE,
  verbose = FALSE,
  gc = FALSE,
  flatten.diag = FALSE,
  standardize.colnames = TRUE,
  tcross.alt.crossprod = FALSE,
  tcross.alt.star = FALSE
)

Arguments

ped: a pedigree dataset. Needs ID, momID, and dadID columns
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
tcross.alt.crossprod: logical. If TRUE, use alternative method of using Crossprod function for computing the transpose
tcross.alt.star: logical. If TRUE, use alternative method of using %\*% for computing the transpose

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.