getInteraction: Retrieve interaction values.

In epinetr: Epistatic Network Modelling with Forward-Time Simulation

Retrieve interaction values.

Description

Retrieve values for an interaction within an epistatic network.

Usage

getInteraction(pop, n)

Arguments

pop	a valid population object
n	the interaction to return

Details

This function returns a k-dimensional array for a particular interaction, where k is the order of interaction and the array holds 3^k entries . This means that a 5-way interaction, for example, will return a 5-dimensional array consisting of 3^5 = 243 entries.

Within each dimension, the three indices (1, 2 and 3) correspond to the homozygous genotype coded 0/0, the heterozygous genotype and the homozygous genotype coded 1/1, respectively. Each entry is drawn from a normal distribution. (Any offset needs to be applied manually using getEpiOffset.)

Author(s)

Dion Detterer, Paul Kwan, Cedric Gondro

See Also

attachEpiNet, getEpiOffset

Examples

# Construct a new population
pop <- Population(
  popSize = 150, map = map100snp, QTL = 20,
  alleleFrequencies = runif(100), broadH2 = 0.7,
  narrowh2 = 0.45, traitVar = 40
)

# Attach additive effects
pop <- addEffects(pop)

# Attach a network of epistatic effects
pop <- attachEpiNet(pop)

# Retrieve the possible values for the first two-way interaction
getInteraction(pop, 1)

# Retrieve the value for the case where, in the fourth two-way
# interaction, the first QTL in the interaction is heterozygous
# and the second QTL in the interaction is the homozygous
# reference genotype.
getInteraction(pop, 4)[2, 1]

# Retrieve the value for the case where, in the second two-way
# interaction, the first QTL in the interaction is the homozygous
# reference genotype and the second QTL in the interaction is the
# homozygous alternative genotype.
getInteraction(pop, 2)[1, 3]

epinetr documentation built on March 18, 2022, 7:01 p.m.