mpMap2 (version 1.0.0)

eightParentPedigreeSingleFunnel: Generate an eight-parent pedigree, using a single funnel

Description

Generate a eight-parent pedigree starting from inbred founders, using a single funnel.

Usage

eightParentPedigreeSingleFunnel(
  initialPopulationSize,
  selfingGenerations,
  nSeeds = 1L,
  intercrossingGenerations
)

Arguments

initialPopulationSize

The number of initially generated lines, whose genetic material is a mosaic of the eight founding lines. These lines are generated using three generations of structured mating.

selfingGenerations

The number of selfing generations at the end of the pedigree.

nSeeds

The number of progeny taken from each intercrossing line, or from each initially generated line (if no intercrossing is specified). These lines are then selfed according to selfingGenerations.

intercrossingGenerations

The number of generations of random mating performed from the F1 generation. Population size is maintained at that specified by initialPopulationSize.

Value

An object of class detailedPedigree representing the experimental design, suitable for simulation using simulateMPCross.

See Also

eightParentPedigreeSingleFunnel, fourParentPedigreeSingleFunnel, fourParentPedigreeRandomFunnels, twoParentPedigree

Examples

# NOT RUN {
pedigree <- eightParentPedigreeSingleFunnel(initialPopulationSize = 10, 
	selfingGenerations = 0, nSeeds = 1, intercrossingGenerations = 1)
map <- qtl::sim.map()
cross <- simulateMPCross(map = map, pedigree = pedigree, mapFunction = haldane)
#Get out a list of funnels, which are rows of this matrix. For this pedigree, every funnel is 1:8. 
getAllFunnels(cross)
#convert the pedigree to a graph
pedigreeAsGraph <- pedigreeToGraph(pedigree)
#Plot it
# }
# NOT RUN {
plot(pedigreeAsGraph)
# }
# NOT RUN {
#Write it to a file in DOT format
# }
# NOT RUN {
write.graph(graph = pedigreeAsGraph@graph, format = "dot", file = "./pedigree.dot")
# }