lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals

BMC Bioinformatics
Andrey ZiyatdinovJosé Manuel Soria

Abstract

Quantitative trait locus (QTL) mapping in genetic data often involves analysis of correlated observations, which need to be accounted for to avoid false association signals. This is commonly performed by modeling such correlations as random effects in linear mixed models (LMMs). The R package lme4 is a well-established tool that implements major LMM features using sparse matrix methods; however, it is not fully adapted for QTL mapping association and linkage studies. In particular, two LMM features are lacking in the base version of lme4: the definition of random effects by custom covariance matrices; and parameter constraints, which are essential in advanced QTL models. Apart from applications in linkage studies of related individuals, such functionalities are of high interest for association studies in situations where multiple covariance matrices need to be modeled, a scenario not covered by many genome-wide association study (GWAS) software. To address the aforementioned limitations, we developed a new R package lme4qtl as an extension of lme4. First, lme4qtl contributes new models for genetic studies within a single tool integrated with lme4 and its companion packages. Second, lme4qtl offers a flexible framework for scenar...Continue Reading

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May 7, 2016·Bioinformatics·Andrey ZiyatdinovJose Manuel Soria

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Citations

Sep 13, 2019·G3 : Genes - Genomes - Genetics·Daniel Runcie, Hao Cheng
May 14, 2019·Alzheimer's & Dementia : Diagnosis, Assessment & Disease Monitoring·Thomas M Lancaster
Oct 28, 2019·Frontiers in Genetics·Juan de Toro-MartínMarie-Claude Vohl
Jul 29, 2020·Molecular Psychiatry·Johan H ThygesenElvira Bramon
Aug 21, 2020·Proceedings of the National Academy of Sciences of the United States of America·Lisa Ann GerdesLuisa Klotz
Oct 3, 2018·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Maris AlverTõnu Esko
Oct 22, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Burcu AlptekinJamie Sherman
Dec 19, 2020·American Journal of Physical Anthropology·Carmen Alonso-LlamazaresAntonio F Pardiñas
Dec 7, 2020·Biological Psychiatry·Lorenza Dall'AglioOliver Pain
Nov 24, 2020·Neurobiology of Aging·Amy N MurrayThomas M Lancaster
Feb 20, 2021·Genetic Epidemiology·Xiang ZhanJun Chen
Apr 16, 2020·Trends in Genetics : TIG·Youqiong YeLeng Han
Apr 29, 2021·Chronobiology International·S L EvansM von Schantz
Jul 6, 2021·Frontiers in Genetics·Diana Caamal-PatMario Vázquez-Peña
Sep 7, 2018·Science Translational Medicine·Emmanuel ClaveUNKNOWN Milieu Intérieur Consortium
Sep 16, 2021·Human Molecular Genetics·David M HowardCathryn M Lewis
Dec 7, 2021·Microbial Genomics·Pakorn AiewsakunArunee Thitithanyanont

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Software Mentioned

lme4qtl
RLRsim
lme4 R
lme4qtl R
pedigreemm R package
R
coxme
assocLmer
Gaston
pedigreemm

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