MCIBD-package: Monte Carlo Identity-By-Descent Matrix Estimation
In MCIBD: Monte Carlo Identity-By-Descent Matrix Estimation

Description Details Author(s) References

MCIBD is a package implemented for flexible identity-by-descent (IBD) matrix estimation in F2 pedigrees. The IBD matrix estimate is approached by a Monte Carlo strategy, where the segregation of founder alleles is easy to define. Epistatic IBD matrices can also be calculated for two arbitrary loci. Such IBD matrix estimates are typically used in variance component quantitative trait loci (QTL) analysis. Parallelization is implemented to enhance the performance of Monte Carlo sampling.

Package:	MCIBD
Type:	Package
Version:	0.4
Date:	2010-08-26
License:	Unlimited
Depends:	`sfsmisc`
Suggests:	`snow, snowfall`

Xia Shen

Maintainer: Xia Shen <xia.shen@lcb.uu.se>

Andersson, L., Haley, C.S., Ellegren, H., Knott, S.A., Johansson, M., Andersson, K., Andersson-Eklund L., Edfors-Lilja, I., Fredholm, M., Hansson, I., Hakansson, J. and Lundstrom, K. (1994). Genetic Mapping of Quantitative Trait Loci for Growth and Fatness in Pigs. Science, 263: 1771-1774.

Nettelblad, C., Holmgren, S., Crooks, L. and Carlborg, O. (2009). cnF2freq: Efficient Determination of Genotype and Haplotype Probabilities in Outbred Populations Using Markov Models. Lecture Notes in Bioinformatics (LNBI), 5462: 307-319, Springer-Verlag Berlin Heidelberg.

Shen, X., Nettelblad, C., Ronnegard, L. and Carlborg, O. (2009). Flexible Identity-By-Descent Matrix Estimation with Given Base Generation Structures in F2 Intercross Designs. Package Vignette.

Shen, X., Ronnegard, L. and Carlborg, O. (2009). Evaluating A Full Likelihood Approach for Variance Component Quantitative Trait Loci Analyses. Submitted.