recodeSex: Recodes Sex Variable in a Pedigree Dataframe

In R-Computing-Lab/BGMisc: An R Package for Extended Behavior Genetics Analysis

Recodes Sex Variable in a Pedigree Dataframe

Description

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_

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.

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.

See Also

plotPedigree

R-Computing-Lab/BGMisc documentation built on April 3, 2025, 3:12 p.m.