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Convert a sex indicator to a standardized code

Source: R/convertSexCodes.R
convertSexCodes.Rd

Part of Pedigree Curation

Usage

convertSexCodes(sex, ignoreHerm = TRUE)

Arguments

sex

character vector or factor of sex codes (see above) for individuals; any other value is treated as unknown.

ignoreHerm

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

Value

A single factor with levels F, M, H and U holding the standardized sex codes after transformation from non-standard codes. Level H is used only when ignoreHerm = FALSE.

Details

Standard sex codes are

  • F – replacing "FEMALE" or "2"

  • M – replacing "MALE" or "1"

  • H – replacing "HERMAPHRODITE" or "4", if ignoreHerm == FALSE

  • U – replacing "HERMAPHRODITE" or "4", if ignoreHerm == TRUE

  • U – replacing "UNKNOWN" or "3"

  • U – replacing a missing, blank or unrecognized value

Case and any spaces around a code are ignored, so " male " and "M " both become M.

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