degree_of_monotonicity {gpmap}R Documentation

Degree of monotonicity of GP map

Description

Functions for computing degree of monotonicity mm for gpmap objects.

Usage

 
  degree_of_monotonicity(gpmap) 
  degree_of_monotonicity_single(gpmap) 

Arguments

gpmap

A gpmap object

Details

degree_of_monotonicity works for any gpmap object (values is (3N)xK(3^N)xK matrix of genotypic values) and calls the internal function degree_of_monotonicity_single for each column. degree_of_monotonicity_single computes substitution effect, locus weights and per-locus and overall degree of monotonicity as decribed in Gjuvsland et al. (2013).

Value

degree_of_monotonicity returns the input gpmap with the following added fields:

degree.monotonicity

Overall degree of monotonicity for the KK GP maps

degree.monotonicity.locus

Data frame with per locus degree of monotonicity for the KK GP maps

locus.weight

Data frame with locus weigths

Author(s)

Arne B. Gjuvsland <arne.gjuvsland@nmbu.no> and Yunpeng Wang <yunpeng.wng@gmail.com>

References

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]

Examples

data(GPmaps)

#Additive GP map is monotone 
degree_of_monotonicity(A)

#Pure AxA epistasis map
degree_of_monotonicity(AA)

#two-locus example in Cheverud & Routman (1995)
degree_of_monotonicity(mouseweight)

[Package gpmap version 0.1.2 Index]