correctParentSex: Correct the sex of animals listed as a sire or dam

In nprcgenekeepr: Genetic Tools for Colony Management

Correct the sex of animals listed as a sire or dam

Description

Part of Pedigree Curation

Usage

correctParentSex(id, sire, dam, sex, recordStatus, reportErrors = FALSE)

Arguments

id	character vector with unique identifier for an individual
sire	character vector with unique identifier for an individual's father (NA if unknown).
dam	character vector with unique identifier for an individual's mother (NA if unknown).
sex	factor with levels: "M", "F", "U". Sex specifier for an individual.
recordStatus	character vector with value of "added" or "original", which indicates whether an animal was added or an original animal.
reportErrors	logical value if TRUE will scan the entire file and make a list of all errors found. The errors will be returned in a list of list where each sublist is a type of error found.

Details

Only true female-sires ("F") and male-dams ("M") are corrected (to "M" and "F" respectively). Parents recorded as hermaphrodite ("H") or unknown ("U") sex are left unchanged, consistent with reportErrors = TRUE mode, which does not flag them.

Value

When reportErrors = FALSE, a factor (or character vector) of corrected sex codes with levels "M", "F", "H", and "U" for the ids provided. When reportErrors = TRUE, a named list of error vectors with elements sireAndDam, femaleSires, and maleDams (each NULL when no such errors are found).

Examples

library(nprcgenekeepr)
pedOne <- data.frame(
  id = c("s1", "d1", "s2", "d2", "o1", "o2", "o3", "o4"),
  sire = c(NA, "s0", "s4", NA, "s1", "s1", "s2", "s2"),
  dam = c(NA, "d0", "d4", NA, "d1", "d2", "d2", "d2"),
  sex = c("F", "F", "M", "F", "F", "F", "F", "M"),
  recordStatus = rep("original", 8),
  stringsAsFactors = FALSE
)
pedTwo <- data.frame(
  id = c("s1", "d1", "s2", "d2", "o1", "o2", "o3", "o4"),
  sire = c(NA, "s0", "s4", NA, "s1", "s1", "s2", "s2"),
  dam = c("d0", "d0", "d4", NA, "d1", "d2", "d2", "d2"),
  sex = c("M", "M", "M", "F", "F", "F", "F", "M"),
  recordStatus = rep("original", 8),
  stringsAsFactors = FALSE
)
pedOneCorrected <- pedOne
pedOneCorrected$sex <- correctParentSex(
  pedOne$id, pedOne$sire, pedOne$dam,
  pedOne$sex, pedOne$recordStatus
)
pedOne[pedOne$sex != pedOneCorrected$sex, ]
pedOneCorrected[pedOne$sex != pedOneCorrected$sex, ]

pedTwoCorrected <- pedTwo
pedTwoCorrected$sex <- correctParentSex(
  pedTwo$id, pedTwo$sire, pedTwo$dam,
  pedTwo$sex, pedOne$recordStatus
)
pedTwo[pedTwo$sex != pedTwoCorrected$sex, ]
pedTwoCorrected[pedTwo$sex != pedTwoCorrected$sex, ]

nprcgenekeepr documentation built on July 26, 2026, 5:06 p.m.