Sets sex for animals listed as either a sire or dam.

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.

Value

A factor with levels: "M", "F", "H", and "U" representing the sex codes for the ids provided

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, ]
#>   id sire  dam sex recordStatus
#> 1 s1 <NA> <NA>   F     original
pedOneCorrected[pedOne$sex != pedOneCorrected$sex, ]
#>   id sire  dam sex recordStatus
#> 1 s1 <NA> <NA>   M     original

pedTwoCorrected <- pedTwo
pedTwoCorrected$sex <- correctParentSex(
  pedTwo$id, pedTwo$sire, pedTwo$dam,
  pedTwo$sex, pedOne$recordStatus
)
pedTwo[pedTwo$sex != pedTwoCorrected$sex, ]
#>   id sire dam sex recordStatus
#> 2 d1   s0  d0   M     original
pedTwoCorrected[pedTwo$sex != pedTwoCorrected$sex, ]
#>   id sire dam sex recordStatus
#> 2 d1   s0  d0   F     original