R/qtlbim

QTL with Bayesian Interval Mapping in experimental crosses

Brian S. Yandell, Tapan Mehta, Samprit Banerjee, Daniel Shriner, Ramprasad Venkataraman, Jee Young Moon, W. Whipple Neely, Hao Wu, Randy von Smith, Nengjun Yi

Research output: Contribution to journalArticle

68 Citations (Scopus)

Abstract

Summary: R/qtlbim is an extensible, interactive environment for the Bayesian Interval Mapping of QTL, built on top of R/qtl (Broman et al., 2003), providing Bayesian analysis of multiple interacting quantitative trait loci (QTL) models for continuous, binary and ordinal traits in experimental crosses. It includes several efficient Markov chain Monte Carlo (MCMC) algorithms for evaluating the posterior of genetic architectures, i.e. the number and locations of QTL, their main and epistatic effects and gene-environment interactions. R/qtlbim provides extensive informative graphical and numerical summaries, and model selection and convergence diagnostics of the MCMC output, illustrated through the vignette, example and demo capabilities of R (R Development Core Team 2006).

Original languageEnglish (US)
Pages (from-to)641-643
Number of pages3
JournalBioinformatics
Volume23
Issue number5
DOIs
StatePublished - Mar 2007
Externally publishedYes

Fingerprint

Quantitative Trait Loci
Markov processes
Markov Chains
Interval
Genetic Epistasis
Gene-environment Interaction
Gene-Environment Interaction
Markov Chain Monte Carlo Algorithms
Bayes Theorem
Genes
Bayesian Analysis
Markov Chain Monte Carlo
Model Selection
Diagnostics
Binary
Output
Model

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Yandell, B. S., Mehta, T., Banerjee, S., Shriner, D., Venkataraman, R., Moon, J. Y., ... Yi, N. (2007). R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses. Bioinformatics, 23(5), 641-643. https://doi.org/10.1093/bioinformatics/btm011

R/qtlbim : QTL with Bayesian Interval Mapping in experimental crosses. / Yandell, Brian S.; Mehta, Tapan; Banerjee, Samprit; Shriner, Daniel; Venkataraman, Ramprasad; Moon, Jee Young; Neely, W. Whipple; Wu, Hao; von Smith, Randy; Yi, Nengjun.

In: Bioinformatics, Vol. 23, No. 5, 03.2007, p. 641-643.

Research output: Contribution to journalArticle

Yandell, BS, Mehta, T, Banerjee, S, Shriner, D, Venkataraman, R, Moon, JY, Neely, WW, Wu, H, von Smith, R & Yi, N 2007, 'R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses', Bioinformatics, vol. 23, no. 5, pp. 641-643. https://doi.org/10.1093/bioinformatics/btm011
Yandell BS, Mehta T, Banerjee S, Shriner D, Venkataraman R, Moon JY et al. R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses. Bioinformatics. 2007 Mar;23(5):641-643. https://doi.org/10.1093/bioinformatics/btm011
Yandell, Brian S. ; Mehta, Tapan ; Banerjee, Samprit ; Shriner, Daniel ; Venkataraman, Ramprasad ; Moon, Jee Young ; Neely, W. Whipple ; Wu, Hao ; von Smith, Randy ; Yi, Nengjun. / R/qtlbim : QTL with Bayesian Interval Mapping in experimental crosses. In: Bioinformatics. 2007 ; Vol. 23, No. 5. pp. 641-643.
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