nprcgenekeepr (version 2.0.0)

getFileDirectRelatives: Get the direct relatives of selected animals from a pedigree file

Description

File-sourced sibling of getLkDirectRelatives: reads a pedigree file through the internal getPedigreeSource() "file" provider (via getPedigree), then delegates the pedigree walk to the source-agnostic getPedDirectRelatives. The result is the full connected pedigree component (ancestors, descendants, and collaterals such as siblings and mates) reachable from the focal animals. It is fully offline and deterministic.

Usage

getFileDirectRelatives(
  ids,
  fileName = NULL,
  sep = ",",
  unrelatedParents = FALSE
)

Value

A data.frame with pedigree structure containing all direct relatives -- the full connected pedigree component (ancestors, descendants, and collaterals) -- for the Ids provided.

Arguments

ids

character vector of animal IDs

fileName

path to a pedigree file (CSV or Excel) read via getPedigree; the file must provide at least id, sire, and dam columns.

sep

column separator passed to the file reader for delimited text files (default ","); ignored for Excel files.

unrelatedParents

logical vector when FALSE the unrelated parents of offspring do not get a record as an ego; when TRUE a place holder record where parent (sire, dam) IDs are set to NA.

Details

Unlike the LabKey source, which fails soft (returns NULL) when its fetch fails, the file source errors loudly: a NULL or missing fileName, a file that does not exist, or a file lacking the id, sire, and dam columns each raises an error.

See Also

Other direct relatives: getLkDirectAncestors(), getLkDirectRelatives(), getPedDirectRelatives()

Examples

library(nprcgenekeepr)
## Build a tiny pedigree file, then pull the relatives of a focal animal.
ped <- data.frame(
  id = c("A", "B", "C"), sire = c(NA, NA, "A"), dam = c(NA, NA, "B"),
  stringsAsFactors = FALSE
)
pedFile <- tempfile(fileext = ".csv")
write.csv(ped, pedFile, row.names = FALSE)
getFileDirectRelatives(ids = "C", fileName = pedFile)
unlink(pedFile)