The ped suite: R packages for pedigree analysis

The ped suite is a collection of R packages for pedigree analysis, covering a variety of applications across several fields. The packages are designed to work harmoniously together, often allowing complex tasks to be solved in a few lines of code.

Core packages

At the centre of the ped suite we find the package pedtools, on which all the others depend. In addition, several packages contain basic features often needed in many types of analysis. These are the core packages:

• pedtools: Creating and working with pedigrees and marker data
• forrel: Forensic pedigree analysis and relatedness analysis
• pedprobr: Marker probabilities and pedigree likelihoods
• ribd: Computation of pedigree-based relatedness coefficients
• verbalisr: Textual descriptions of pedigree relationships

Specialised packages

The following packages are devoted to special applications:

• ibdsim2: Simulation of identity-by-descent sharing by family members
• dvir: Disaster victim identification
• pedbuildr: Pedigree reconstruction
• paramlink2: Parametric linkage analysis
• pedmut: Mutation models for pedigree likelihood computations
• segregatr: Segregation analysis for clinical variant interpretation

Retired packages

These packages have been superseded by other packages and are no longer compatible with the rest of the ped suite. They are maintained only for legacy purposes and should not be used in new projects.

• paramlink: This package marked the birth of the ped suite. Originally intended for parametric linkage analysis, it also contained the seeds of the current packages pedtools, pedprobr, ribd and forrel.
• IBDsim: This is replaced by ibdsim2. (Regrettably, the name ‘IBDsim’ is very similar to that of the unrelated (non-R) software ‘IBDSim’ (Leblois, Estoup & Rousset).)

Imported packages

• kinship2: All pedigree plots in the ped suite are internally made by importing the plotting feature of kinship2 (Sinnwell, Therneau & Schaid). Creating nice pedigree plots is a highly non-trivial matter, so if you use the ped suite to make pedigree plots for publications, please also credit kinship2.

QuickPed - an online pedigree creator

In addition to the R packages, the ped suite also includes QuickPed, a free interactive program for creating and exploring pedigrees. Read more about it here, or simply try it out: https://magnusdv.shinyapps.io/quickped.