Take a pedigree and turn it into a common nuclear environmental relatedness matrix

Take a pedigree and turn it into a common nuclear environmental relatedness matrix

Usage

ped2cn(
  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.