Repository files navigation

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

At the centre of thepedsuite we find the packagepedtools, onwhich all the others depend. In addition, several packages contain basicfeatures often needed in many types of analysis. These are thecorepackages:

• pedtools: Creating and workingwith pedigrees and marker data
• forrel: Forensic pedigreeanalysis and relatedness analysis
• pedprobr: Marker probabilitiesand pedigree likelihoods
• ribd: Computation ofpedigree-based relatedness coefficients
• verbalisr: Verbaldescriptions of pedigree relationships

The following packages are devoted to special applications:

• ibdsim2: Simulation ofidentity-by-descent sharing by family members
• dvir: Disaster victimidentification
• ibdfindr: Inferringidentical-by-descent genomic segments from SNP Genotypes
• norSTR: Data package with STRallele frequencies
• paramlink2: Parametriclinkage analysis
• pedbuildr: Pedigreereconstruction
• pedFamilias: Import andexport.fam files used by theFamiliassoftware
• pedmut: Mutation models forpedigree likelihood computations
• segregatr: Segregationanalysis for clinical variant interpretation

These packages have been superseded by other packages and are no longercompatible with the rest of thepedsuite.

• paramlink: Thispackage marked the birth of thepedsuite. Originally intended forparametric linkage analysis, it also contained the seeds of thecurrent packagespedtools,pedprobr,ribd andforrel.
• IBDsim: This is replacedbyibdsim2. (Regrettably, the name ‘IBDsim’ is very similar tothat of the unrelated (non-R) software ‘IBDSim’ (Leblois, Estoup &Rousset).)

• kinship2: Pedigreeplotting in thepedsuite depends onkinship2 (Sinnwell,Therneau & Schaid) for pedigreealignment calculations.

Several Shiny apps based on thepedsuite have been developed. Readmore 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