Converts sex indicator for an individual to a standardized codes.

Source: R/convertSexCodes.R

Part of Pedigree Curation

convertSexCodes(sex, ignoreHerm = TRUE)

Arguments

sex

factor with levels: "M", "F", "U". Sex specifier for an individual.
ignoreHerm

logical flag indicating if hermaphrodites should be treated as unknown sex ("U"), default is TRUE.

Value

A vector of factors representing standardized sex codes after transformation from non-standard codes.

Details

Standard sex codes are

  • F -- replacing "FEMALE" or "2"

  • M -- replacing "MALE" or "1"

  • H -- replacing "HERMAPHRODITE" or "4", if ignore.herm == FALSE

  • U -- replacing "HERMAPHRODITE" or "4", if ignore.herm == TRUE

  • U -- replacing "UNKNOWN" or "3"

Examples

# \donttest{
library(nprcgenekeepr)
original <- c("m", "male", "1", "MALE", "M", "F", "f", "female",
              "FemAle", "U", "Unknown", "H", "hermaphrodite",
              "U", "Unknown", "3", "4")
sexCodes <- convertSexCodes(original)
sexCodes

#>  [1] M M M M M F F F F U U U U U U U U
#> Levels: F M H U
# }