The
pedsuite: R packages for pedigree analysis
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
- dvir: Disaster victim
identification
- paramlink2:
Parametric linkage analysis
- pedbuildr:
Pedigree reconstruction
- pedFamilias:
Import and export
.fam files used by the Familias software
- 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These packages have been superseded by other packages and are no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. They
are maintained only for legacy purposes and should not be used in new
projects.
- 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).)
Imported packages
Shiny apps
Several Shiny apps based on the pedsuite have been
developed. Read more about them here:
- QuickPed:
Interactive pedigree builder and relatedness analyser
- DIVIANA:
Disaster victim identification
- ibdsim2-shiny:
IBD distributions in pedigrees
- KLINK:
Kinship analysis with linked markers
- LinkageLab:
Playing with linked markers
- ibdClassifier:
Classifying relationships based on IBD segments