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Correct the sex of animals listed as a sire or dam

Source: R/correctParentSex.R
correctParentSex.Rd

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 or character vector of sex codes ("M", "F", "H", "U"). Sex specifier for an individual. A character input returns a character vector.

recordStatus

character vector with value of "added" or "original", which indicates whether an animal was added or an original animal. Only "added" is special: an NA, blank or unrecognized value is treated as an original animal, and NULL means no added records are known. It is used only when reportErrors = TRUE.

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. When FALSE, an ID listed as both a sire and a dam stops with an error; when TRUE it is returned as sireAndDam.

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).

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.

When reportErrors = TRUE, only records whose recordStatus is exactly "added" are left out of the report. A missing (NA), blank or unrecognized status is treated as an original animal, and a NULL recordStatus means no added records are known, so every animal is checked.

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$sex, pedTwo$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