Converts sex indicator for an individual to a standardized codes.

Part of Pedigree Curation

Usage

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

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