GENLIB

GENLIB provides functions to analyze and simulate large-scale genealogical datasets to quantify kinship, inbreeding coefficients, genetic contributions, and identical-by-descent (IBD) sharing in founder populations using data such as the BALSAC database for the French Canadian population of Quebec.

Key Features:

• Data management: Functions to extract segments of a genealogy and select particular individuals for subset analyses.
• Genealogical description and pedigree construction: Tools to describe the size and complexity of genealogies and to construct extended pedigrees.
• Kinship and inbreeding: Computation of kinship coefficients and inbreeding coefficients.
• Genetic contributions: Computation of genetic contributions within pedigrees.
• Gene-dropping simulations: Functions to perform gene-dropping simulations to investigate identical-by-descent (IBD) sharing of alleles and chromosomal segments and to estimate probabilities of IBD sharing.
• Haplotype transmission simulation (gen.simuHaplo): The gen.simuHaplo() function (introduced in version 1.1.9) to simulate transmission of haplotypes from founders to probands across large and complex genealogies.
• Large-dataset support: Compatibility with large genealogical datasets such as the BALSAC database spanning over 3 million records across four centuries.

Scientific Applications:

• Evolutionary and population genetics: Analysis of population structure, relatedness, and genetic transmission in founder populations.
• Demography: Use of deep genealogical records to study demographic histories and lineage complexity.
• Genetic epidemiology: Investigation of the genetic basis of diseases within pedigrees using kinship metrics, genetic contributions, and simulation-based IBD analyses.
• Inheritance and linkage studies: Exploration of inheritance patterns and IBD sharing to inform disease-variant transmission and linkage analyses.

Methodology:

Implemented in R with functions to construct extended pedigrees, describe genealogical size and complexity, compute kinship and inbreeding coefficients and genetic contributions, perform gene-dropping simulations, and run gen.simuHaplo haplotype transmission simulations.