Functions for computing degree of monotonicity m for gpmap objects.
● Data Source:
CranContrib
● Keywords:
● Alias: degree_of_monotonicity, degree_of_monotonicity_single
●
0 images
|
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).
● Data Source:
CranContrib
● Keywords: package
● Alias: gpmap-package
●
0 images
|
generate_gpmap
(Package: gpmap) :
Function for creating genotype-phenotype (GP) maps
Function for creating a gpmap object representing a genotype-phenotype (GP) map for N biallelic loci or more generally K such maps, from a matrix of genotypic values.
● Data Source:
CranContrib
● Keywords:
● Alias: generate_gpmap, gpmap
●
0 images
|
enumerate_genotypes
(Package: gpmap) :
Function for enumerating genotypes for eqn{N
Function for enumerating all 3^N genotypes for N biallelic loci. Optional specification of names of loci and alleles. genotypes. Generates a data frame of multilocus genotypes in the sequence used for objects of class gpmap.
● Data Source:
CranContrib
● Keywords:
● Alias: enumerate_genotypes
●
0 images
|
print.gpmap
(Package: gpmap) :
Print function for code{link{gpmap
Print a summary of a genotype-phenotype (GP) map (an object of class gpmap) with 1-3 N biallelic loci.
● Data Source:
CranContrib
● Keywords:
● Alias: print.gpmap
●
0 images
|
decompose_monotone
(Package: gpmap) :
Decompose genotype-phenotype map(s) using monotone regression
Functions for decomposing genotype-phenotype (GP) maps with N biallelic loci using monotone regression from the isotone package.
● Data Source:
CranContrib
● Keywords:
● Alias: decompose_monotone, decompose_monotone_single
●
0 images
|
partial_genotype_order
(Package: gpmap) :
Generate partial ordering of genotype space based from allele content of genotypes
Generate the strict partial order on genotype space specified in eq. (13) in Gjuvsland et al. (2011). For a genotype space with N biallelic loci a minimal description of this partial order is given by 2N*3^{(N-1)} inequalities.
● Data Source:
CranContrib
● Keywords:
● Alias: partial_genotype_order
●
0 images
|
plot.gpmap
(Package: gpmap) :
Functions for creating lineplots of genotype-phenotype (GP) maps
Function for creating lineplots for genotype-phenotype (GP) map (an object of class gpmap) with 1-3 biallelic loci.
● Data Source:
CranContrib
● Keywords:
● Alias: plot.gpmap, plot.gpmap.decomp.mono
●
0 images
|
monotone_regression
(Package: gpmap) :
Perform monotone regression on a genotype-phenotype (GP) map
The function uses partial_genotype_order and activeSet from the isotone package to do monotone regression (Leeuw et al., 2009) on a GP map.
● Data Source:
CranContrib
● Keywords:
● Alias: monotone_regression
●
0 images
|
providing 
.