eightParentPedigreeRandomFunnels: Generate an eight-parent pedigree, using random funnels

In rohan-shah/mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description

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

Usage

eightParentPedigreeRandomFunnels(
  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

pedigree <- eightParentPedigreeRandomFunnels(initialPopulationSize = 10, 
	selfingGenerations = 0, nSeeds = 1, intercrossingGenerations = 10)
#Generate map
map <- qtl::sim.map()
#Simulate data
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 a random ordering of 1:8. 
getAllFunnels(cross)
#convert the pedigree to a graph
pedigreeAsGraph <- pedigreeToGraph(pedigree)
#Plot it
plot(pedigreeAsGraph)
#Write it to a file in DOT format

rohan-shah/mpMap2 documentation built on July 21, 2020, 8:58 p.m.