Validates and Optionally Repairs Parent IDs in a Pedigree Dataframe

This function takes a pedigree object and performs two main tasks: 1. Checks for the validity of parent IDs, specifically looking for instances where only one parent ID is missing. 2. Optionally repairs the missing parent IDs based on a specified logic.

Usage

checkParentIDs(
  ped,
  verbose = FALSE,
  repair = FALSE,
  repairsex = repair,
  addphantoms = repair,
  parentswithoutrow = repair,
  famID = "famID",
  personID = "ID",
  momID = "momID",
  dadID = "dadID"
)

Arguments

ped

A dataframe representing the pedigree data with columns 'ID', 'dadID', and 'momID'.

verbose

A logical flag indicating whether to print progress and validation messages to the console.

repair

A logical flag indicating whether to attempt repairs on missing parent IDs.

repairsex

A logical flag indicating whether to attempt repairs on sex of the parents

addphantoms

A logical flag indicating whether to add phantom parents for missing parent IDs.

parentswithoutrow

A logical flag indicating whether to add parents without a row in the pedigree.

famID

Character. Column name for family IDs.

personID

Character. Column name for individual IDs.

momID

Character. Column name for maternal IDs.

dadID

Character. Column name for paternal IDs.

Value

Depending on the value of `repair`, either a list containing validation results or a repaired dataframe is returned.

Examples

if (FALSE) { # \dontrun{
ped <- data.frame(ID = 1:4, dadID = c(NA, 1, 1, 2), momID = c(NA, NA, 2, 2))
checkParentIDs(ped, verbose = TRUE, repair = FALSE)
} # }