
Sets sex for animals listed as either a sire or dam.
Source:R/correctParentSex.R
correctParentSex.Rd
Part of Pedigree Curation
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.
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