Creating and Working with Pedigrees and Marker Data
Add allele
Convert pedigree to kinship2 format
Convert ped to data.frame
Convert ped to matrix
Conversions to ped objects
Connected pedigree components
Distribute markers evenly along a set of chromosomes
Expected homozygosity and heterozygosity
Extract singletons from pedigree
Family identifier
Inbreeding coefficients of founders
Allele frequency database
Allele matrix manipulation
Pedigree component
Genotype matrix
Tabulate marker positions
Get or set the sex of pedigree members
Harmonise markers across components in a ped list
Pedigree loops
Test if something is a marker
Is an object a ped object?
Find homozygous genotypes
Get or set locus attributes
Attach markers to pedigrees
Get marker attributes
Set marker attributes
Marker properties
Select or remove attached markers
Set marker attributes
Marker objects
Mask and unmask pedigree datasets
Check for Mendelian errors
Merge two pedigrees
Internal marker constructor
Internal ped constructor
The number of markers attached to a pedigree
Create basic pedigrees
Complex pedigree structures
Internal ordering of pedigree members
Add/remove pedigree members
Pedigree subgroups
Pedigree utilities
Pedigree construction
pedtools: Creating and Working with Pedigrees and Marker Data
Plot pedigree
Internal plot methods
Plot a collection of pedigrees.
S3 methods
Printing pedigrees
Random pedigree
Read a pedigree from file
Get or modify pedigree labels
Find markers for which two individuals have the same genotype
Set a mutation model
Attach SNP loci to a pedigree
Sort the alleles in each genotype
Swap genotypes between individuals
Transfer marker data
Pedigree errors
Write a pedigree to file
A comprehensive collection of tools for creating, manipulating and visualising pedigrees and genetic marker data. Pedigrees can be read from text files or created on the fly with built-in functions. A range of utilities enable modifications like adding or removing individuals, breaking loops, and merging pedigrees. An online tool for creating pedigrees interactively, based on 'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>. 'pedtools' is the hub of the 'pedsuite', a collection of packages for pedigree analysis. A detailed presentation of the 'pedsuite' is given in the book 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).