The pedsuite 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 pedsuite 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:
Verbal descriptions of pedigree relationships
Specialised packages
The following packages are devoted to special applications:
ibdsim2:
Simulation of identity-by-descent sharing by family members
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These packages have been superseded by other packages and are no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 pedsuite.
paramlink: This
package marked the birth of the pedsuite. 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).)
