Description Usage Arguments Details Value Examples
View source: R/getAllFunnels.R
Get every order of the founding lines, which makes a contribution to the final population
1 | getAllFunnelsIncAIC(cross, standardised = FALSE)
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cross |
The object of class |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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,]
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