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Validates and Optionally Repairs Sex Coding in a Pedigree Dataframe

Source: R/checkSex.R
checkSex.Rd

This function checks and optionally modifies the coding of the biological 'sex' variable in a pedigree dataset. It serves two primary purposes: 1. Recodes the 'sex' variable based on specified codes for males and females, if provided. 2. Identifies and optionally repairs inconsistencies in sex coding that could break the algorithm for constructing genetic pedigrees.

Usage

checkSex(
  ped,
  code_male = NULL,
  code_female = NULL,
  verbose = FALSE,
  repair = FALSE
)

Arguments

ped

A dataframe representing the pedigree data with a 'sex' column.

code_male

The current code used to represent males in the 'sex' column.

code_female

The current code used to represent females in the 'sex' column. If both are NULL, no recoding is performed.

verbose

A logical flag indicating whether to print progress and validation messages to the console.

repair

A logical flag indicating whether to attempt repairs on the sex coding.

Value

Depending on the value of `repair`, either a list containing validation results or a repaired dataframe is returned.

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.

Examples

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