getAllFunnelsIncAIC: Get all funnels, including AIC lines
In rohan-shah/mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description Usage Arguments Details Value Examples

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

1	getAllFunnelsIncAIC(cross, standardised = FALSE)

`cross`	The object of class `mpcross` containing the pedigree of interest
`standardised`	Should the output funnels be standardised?

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.

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

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,]