Add unilineal parental ancestor chains to a pedigree

Adds an ordered unilineal parental ancestor chain for each individual in a pedigree. The chain can follow either paternal links only or maternal links only.

Usage

addParentalChain(
  ped,
  personID = "personID",
  dadID = "dadID",
  momID = "momID",
  chain_col = "chain",
  chain_string_col = "chain_string",
  collapse = "|",
  component = c("dadID", "momID"),
  traversal_direction = "in"
)

Arguments

ped

A pedigree data frame.

personID

Character string giving the name of the column containing individual IDs.

dadID

Character string giving the name of the column containing paternal IDs.

momID

Character string giving the name of the column containing maternal IDs.

chain_col

Character string giving the name of the output list-column that will contain the ordered parental ancestor chain for each individual.

chain_string_col

Character string giving the name of the output character column that will contain the collapsed parental ancestor chain.

collapse

Character string used to collapse ancestor IDs into `chain_string_col`.

component

Character string specifying which parental component to follow. Must be either `"dadID"` for paternal chains or `"momID"` for maternal chains.

traversal_direction

Character giving the mode of transversion: defaults to "in". If set to out, will procedure a list of descendants.

Value

A data frame with two added columns:

`chain_col`

A list-column containing the ordered unilineal parental ancestor chain for each individual.

`chain_string_col`

A character column containing the collapsed ancestor chain, or `NA_character_` when no ancestors are found in the selected component.

Details

For `component = "dadID"`, the chain follows: father, paternal grandfather, paternal great-grandfather, and so on.

For `component = "momID"`, the chain follows: mother, maternal grandmother, maternal great-grandmother, and so on.

The function constructs a parent-specific version of the pedigree, converts it to a graph using [ped2graph()], identifies reachable ancestors for each individual, orders those ancestors by graph distance from the focal individual, and adds both a list-column representation and a collapsed string representation to the original pedigree.

All pedigree IDs used to construct the parent-specific graph are coerced to character. Individuals that are not represented as graph vertices receive an empty chain in `chain_col` and `NA_character_` in `chain_string_col`.

The ordering of each chain is based on graph distance from the focal individual, where distance 1 is the selected parent, distance 2 is the selected parent's same-component parent, and so forth.