| gpmap-package {gpmap} | R Documentation |
Tools for analysing and plotting genotype-phenotype maps
Description
The gpmap package deals with genotype-phenotype maps for biallelic loci underlying
quantitative phenotypes. The package provides a class gpmaps, analysis functions and basic
lineplots. The package is designed for studying the properties of GP maps without
reference to any particular population, i.e. the physiological (Cheverud & Routman, 1995)
or functional (Hansen, 2001) properties of the GP map. This is opposed to statistical effects underlying
most of quantitative genetics, where the GP-map is analysed togehter with genotype frequencies in a given
population (e.g. Lynch & Walsh, 1998).
In version 0.1 which is released as part of the publication of Gjuvsland et al. (2013) we have implemented functionality for studying monotonicity Gjuvsland et al. (2011) of GP maps. The package utilizes the isotone package for monotone regression, and the foreach package for parallel computation.
The package consists of the following high-level functions :
enumerate_genotypes, generate_gpmap,
degree_of_monotonicity, decompose_monotone and
plot.gpmap
Author(s)
Arne B. Gjuvsland <arne.gjuvsland@nmbu.no> and Yunpeng Wang <yunpeng.wng@gmail.com>
References
Cheverud JM & Routman EJ (1995) Epistasis and Its Controbution to Genetic Variance Components. Genetics 139:1455-1461 [link]
Gjuvsland AB, Vik JO, Woolliams JA, Omholt SW (2011) Order-preserving principles underlying genotype-phenotype maps ensure high additive proportions of genetic variance. Journal of Evolutionary Biology 24(10):2269-2279 [link]
Gjuvsland AB, Wang Y, Plahte E and Omholt SW (2013) Monotonicity is a key feature of genotype-phenotype maps. Front. Genet. 4:216. doi: 10.3389/fgene.2013.00216 [link]
Hansen T & Wagner GP (2001) Modeling genetic Architecture: A Multilinear Theory of gene Interaction. Theoretical Population Biology 59:61-86 [link]
Leeuw J, Hornik K and Mair P (2009) Isotone Optimization in R: Pool-Adjacent-Violators Algorithm (PAVA) and Active Set Methods. Journal of Statistical Software 32(5) [link]
Lynch M & Walsh B (1998) Genetics and Analysis of Quantitative Traits, Sunderland, MA: Sinauer Associates