Constellation, le dépôt institutionnel de l'Université du Québec à Chicoutimi

GENLIB : an R package for the analysis of genealogical data

Gauvin Héloïse, Lefebvre Jean-François, Moreau Claudia, Lavoie Eve-Marie, Labuda Damian, Vézina Hélène et Roy-Gagnon Marie-Hélène. (2015). GENLIB : an R package for the analysis of genealogical data. BMC Bioinformatics, 16, (1),

[thumbnail of s12859-015-0581-5.pdf]
Prévisualisation
PDF - Version publiée
1MB

URL officielle: https://dx.doi.org/doi:10.1186/s12859-015-0581-5

Résumé

Background

Founder populations have an important role in the study of genetic diseases. Access to detailed genealogical records is often one of their advantages. These genealogical data provide unique information for researchers in evolutionary and population genetics, demography and genetic epidemiology. However, analyzing large genealogical datasets requires specialized methods and software. The GENLIB software was developed to study the large genealogies of the French Canadian population of Quebec, Canada. These genealogies are accessible through the BALSAC database, which contains over 3 million records covering the whole province of Quebec over four centuries. Using this resource, extended pedigrees of up to 17 generations can be constructed from a sample of present-day individuals.

Results

We have extended and implemented GENLIB as a package in the R environment for statistical computing and graphics, thus allowing optimal flexibility for users. The GENLIB package includes basic functions to manage genealogical data allowing, for example, extraction of a part of a genealogy or selection of specific individuals. There are also many functions providing information to describe the size and complexity of genealogies as well as functions to compute standard measures such as kinship, inbreeding and genetic contribution. GENLIB also includes functions for gene-dropping simulations.

The goal of this paper is to present the full functionalities of GENLIB. We used a sample of 140 individuals from the province of Quebec (Canada) to demonstrate GENLIB’s functions. Ascending genealogies for these individuals were reconstructed using BALSAC, yielding a large pedigree of 41,523 individuals. Using GENLIB’s functions, we provide a detailed description of these genealogical data in terms of completeness, genetic contribution of founders, relatedness, inbreeding and the overall complexity of the genealogical tree. We also present gene-dropping simulations based on the whole genealogy to investigate identical-by-descent sharing of alleles and chromosomal segments of different lengths and estimate probabilities of identical-by-descent sharing.

Conclusions

The R package GENLIB provides a user friendly and flexible environment to analyze extensive genealogical data, allowing an efficient and easy integration of different types of data, analytical methods and additional developments and making this tool ideal for genealogical analysis.

Type de document:Article publié dans une revue avec comité d'évaluation
ISSN:1471-2105
Volume:16
Numéro:1
Version évaluée par les pairs:Oui
Date:2015
Identifiant unique:10.1186/s12859-015-0581-5
Sujets:Sciences sociales et humaines > Sciences humaines > Histoire
Sciences sociales et humaines > Sciences sociales > Démographie
Sciences naturelles et génie > Sciences mathématiques > Informatique
Département, module, service et unité de recherche:Départements et modules > Département des sciences humaines
Mots-clés:genealogical data, founder populations, software, historical demography, kinship, inbreeding, genetics, gene-dropping simulations
Déposé le:08 oct. 2022 14:59
Dernière modification:08 oct. 2022 14:59
Afficher les statistiques de telechargements

Éditer le document (administrateurs uniquement)

Creative Commons LicenseSauf indication contraire, les documents archivés dans Constellation sont rendus disponibles selon les termes de la licence Creative Commons "Paternité, pas d'utilisation commerciale, pas de modification" 2.5 Canada.

Bibliothèque Paul-Émile-Boulet, UQAC
555, boulevard de l'Université
Chicoutimi (Québec)  CANADA G7H 2B1
418 545-5011, poste 5630