degree_of_monotonicity {gpmap}

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

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).

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

Author(s)

Arne B. Gjuvsland <[e-mail]> and Yunpeng Wang <[e-mail]>

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)