mpMap2 (version 1.0.4)

getAllFunnelsIncAIC: Get all funnels, including AIC lines

Description

Get every order of the founding lines, which makes a contribution to the final population

Usage

getAllFunnelsIncAIC(cross, standardised = FALSE)

Arguments

cross

The object of class mpcross containing the pedigree of interest

standardised

Should the output funnels be standardised?

Value

Matrix of mixing orders that contribute to the final popluation. Rows DO NOT refer to specific genetic lines.

Details

This function is similar to getAllFunnels, but more useful for populations with maintenance (or AIC) generations. It returns a list of all the mixing orders in the initial generations, which make a genetic contribution to the final population. Unlike for getAllFunnels, rows of the returned matrix DO NOT refer to specific genetic lines.

Examples

# NOT RUN {
set.seed(1)
pedigree <- fourParentPedigreeRandomFunnels(initialPopulationSize = 1000,
     selfingGenerations = 6, intercrossingGenerations = 1)
#Assume infinite generations of selfing in subsequent analysis
selfing(pedigree) <- "infinite"
#Generate random map
map <- qtl::sim.map(len = 100, n.mar = 101, anchor.tel = TRUE, include.x = FALSE)
#Simulate data
cross <- simulateMPCross(map = map, pedigree = pedigree, mapFunction = haldane, seed = 1L)
#Because we have maintenance in this experiment, we can't get out the funnels per genetic line
funnels <- getAllFunnels(cross)
dim(funnels)
funnels[1:10,]
#But we can get out a list of all the funnels that go into the experiment.
funnels <- getAllFunnelsIncAIC(cross)
dim(funnels)
funnels[1:10,]
# }