gpmap (version 0.1.2)

degree_of_monotonicity: Degree of monotonicity of GP map

Description

Functions for computing degree of monotonicity \(m\) for gpmap objects.

Usage

degree_of_monotonicity(gpmap) 
  degree_of_monotonicity_single(gpmap)

Arguments

gpmap

A gpmap object

Value

degree_of_monotonicity returns the input gpmap with the following added fields:

degree.monotonicity

Overall degree of monotonicity for the \(K\) GP maps

degree.monotonicity.locus

Data frame with per locus degree of monotonicity for the \(K\) GP maps

locus.weight

Data frame with locus weigths

Details

degree_of_monotonicity works for any gpmap object (values is \((3^N)xK\) 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).

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

# NOT RUN {
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)
# }