getEpistasis {epinetr}

Calculate epistatic interactions.

Description

Calculate epistatic interactions for members of the population.

Usage

getEpistasis(pop, scale = TRUE, geno = NULL)

Arguments

pop

a valid Population object with epistatic effects attached

scale

a boolean value indicating whether to scale the values to bring them in line with the desired initial variance

geno

by default, the function uses the current genotypes in the population; alternatively, geno is a user-supplied set of genotypes (limited to QTLs) on which to base the calculation

Details

This function calculates the values of each epistatic interaction per individual, returning a matrix whose rows are the individuals in the population and whose columns are the epistatic interactions. The sums of these rows represent the total epistatic contribution to the phenotype, once the epistatic offset is added.

Author(s)

Dion Detterer, Paul Kwan, Cedric Gondro

See Also

getEpiOffset

Examples

# Construct a new population with epistatic effects
pop <- Population(
  popSize = 20, map = map100snp, QTL = 20,
  broadH2 = 0.4, narrowh2 = 0, traitVar = 40,
  alleleFrequencies = runif(100, 0.05, 0.5)
)
pop <- attachEpiNet(pop)

# Find the epistatic contribution to the individuals' phenotypes
rowSums(getEpistasis(pop)) + getEpiOffset(pop)

# Compare with epistatic component from getComponents()
getComponents(pop)$Epistatic