Repairs Sex Coding in a Pedigree Dataframe

This function serves as a wrapper around `checkSex` to specifically handle the repair of the sex coding in a pedigree dataframe.

Usage

repairSex(ped, verbose = FALSE, code_male = NULL)

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.

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

The validation process identifies: - The unique sex codes present in the dataset. - Whether individuals listed as fathers or mothers have inconsistent sex codes. - Instances where an individual's recorded sex does not align with their parental role.

If `repair = TRUE`, the function standardizes sex coding by: - Assigning individuals listed as fathers the most common male code in the dataset. - Assigning individuals listed as mothers the most common female code.

This function uses the terms 'male' and 'female' in a biological context, referring to chromosomal and other biologically-based characteristics necessary for constructing genetic pedigrees. The biological aspect of sex used in genetic analysis (genotype) is distinct from the broader, richer concept of gender identity (phenotype).

We recognize the importance of using language and methodologies that affirm and respect the full spectrum of gender identities. The developers of this package express unequivocal support for folx in the transgender and LGBTQ+ communities.

See also

checkSex

Examples

if (FALSE) { # \dontrun{
ped <- data.frame(ID = c(1, 2, 3), sex = c("M", "F", "M"))
repairSex(ped, code_male = "M", verbose = TRUE)
} # }