This function serves as is primarily used internally, by plotting functions etc. It sets the `repair` flag to TRUE automatically and forwards any additional parameters to `checkSex`.
Usage
recodeSex(
ped,
verbose = FALSE,
code_male = NULL,
code_na = NULL,
code_female = NULL,
recode_male = "M",
recode_female = "F",
recode_na = NA_character_
)Arguments
- ped
A dataframe representing the pedigree data with a 'sex' column.
- verbose
A logical flag indicating whether to print progress and validation messages to the console.
- code_male
The current code used to represent males in the 'sex' column.
- code_na
The current value used for missing values.
- code_female
The current code used to represent females in the 'sex' column. If both are NULL, no recoding is performed.
- recode_male
The value to use for males. Default is "M"
- recode_female
The value to use for females. Default is "F"
- recode_na
The value to use for missing values. Default is NA_character_
Value
A modified version of the input data.frame ped, containing an additional or modified 'sex_recode' column where the 'sex' values are recoded according to code_male. NA values in the 'sex' column are preserved.
Details
This function uses the terms 'male' and 'female' in a biological context, based on chromosomes and other biologically-based characteristics relevant to genetic studies. This usage is not intended to negate the personal gender identity of any individual.
We recognize the importance of using language and methodologies that affirm and respect all gender identities. While this function focuses on chromosomal information necessary for constructing genetic pedigrees, we affirm that gender is a spectrum, encompassing a wide range of identities beyond the binary. The developers of this package express unequivocal support for folx in the transgender and LGBTQ+ communities. We respect the complexity of gender identity and acknowledge the distinction between the biological aspect of sex used for genetic analysis (genotype) and the broader, richer concept of gender identity (phenotype).