Fuse MZ twin pairs in a pedigree dataset for path tracing This function identifies MZ twin pairs in the pedigree dataset and merges their IDs for path tracing purposes. The second twin in each pair is made a founder (with NA parents), and all children of the second twin are redirected to the first twin. This allows for correct relatedness calculations without diagonal or downstream artifacts.

Usage

fuseTwins(
  ped,
  df_twins = NULL,
  mz_id_pairs = NULL,
  mz_row_pairs = NULL,
  config = list(verbose = FALSE),
  test_df_twins = FALSE,
  beta = FALSE
)

Arguments

ped: A pedigree data.frame with columns ID, momID, dadID, and optionally twinID and zygosity. The function will look for MZ twin pairs based on the twinID column and optionally restrict to MZ pairs if a zygosity column is present.
df_twins: Optional data frame with columns twin1_id, twin2_id, twin1_row, and twin2_row specifying the IDs and row indices of MZ twin pairs to fuse. If provided, this will be used instead of automatically identifying MZ twins from the twinID column. If this parameter is provided, it takes precedence over mz_id_pairs and mz_row_pairs. If test_df_twins is TRUE, this data frame will be returned for testing purposes instead of performing the fusion.
mz_id_pairs: Optional list of length-2 character vectors specifying the IDs of MZ twin pairs to fuse. If provided, this will be used instead of automatically identifying MZ twins from the twinID column. Each element should be a character vector of length 2, e.g. list(c("ID1", "ID2"), c("ID3", "ID4")).
mz_row_pairs: Optional list of length-2 integer vectors specifying the row indices of MZ twin pairs to fuse. If provided, this will be used instead of automatically identifying MZ twins from the twinID column. Each element should be an integer vector of length 2, e.g. list(c(1, 2), c(3, 4)).
config: A list of configuration options.
test_df_twins: logical. If TRUE, return the data frame of twin pairs instead of the modified pedigree. Default is FALSE.
beta: logical. If TRUE, use an optimized approach with O(1) lookups for large pedigrees when identifying MZ twins. Default is FALSE.

Value

A modified version of the input pedigree data.frame with MZ twin pairs fused for path tracing. If test_df_twins is TRUE, returns the data frame of identified twin pairs instead.