fix_pedigree: Function to ensure pedigree is correctly structured for gene...

In simplydch/GeneDrop: Drops Genes Down A Pedigree And Tracks Alleles

Function to ensure pedigree is correctly structured for gene dropping

Description

This function checks the pedigree for potentential problems in structure it reorganises the individuals if neccessary and renames columns to ensure the pedigree is in the correct format for gene-dropping. Sex and Cohort can be included as columns in the pedigree or provided as seperate vectors. It adds in any individuals that are missing and checks sex coding is correct and consistent. It returns the pedigree as a matrix

Usage

fix_pedigree(pedigree, sex = TRUE, cohort = TRUE)

Arguments

pedigree	A dataframe or matrix. A pedigree with ID, Sire and Dam columns.
sex	logical or vector. TRUE if sex column is included in pedigree, otherwise a vector containing the sex of each individual. Defaults to TRUE
cohort	logical or vector. TRUE if cohort column is included in pedigree, otherwise a vector containing the cohort of each individual. Defaults to TRUE

simplydch/GeneDrop documentation built on July 8, 2024, 8:17 p.m.