eightParentPedigreeImproperFunnels: Generate an eight-parent pedigree with improper funnels

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

Description

Generate a eight-parent pedigree starting from inbred founders, where the founders in the funnels are not necessarily distinct.

Usage

eightParentPedigreeImproperFunnels(
  initialPopulationSize,
  selfingGenerations,
  nSeeds
)

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.

Details

Generate a eight-parent pedigree starting from inbred founders. The founders in the funnel for every line are chosen with replacement. So for any line from the final population, it is likely that some founding lines are absent from the corresponding funnel, and some appear multiple times.

Value

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

See Also

eightParentPedigreeSingleFunnel, fourParentPedigreeSingleFunnel, fourParentPedigreeRandomFunnels, twoParentPedigree

Examples

pedigree <- eightParentPedigreeImproperFunnels(initialPopulationSize = 10, 
	selfingGenerations = 0, nSeeds = 1)
#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. Note that, of the values 1:8, 
#    some are missing within a row, and some are repeated. 
getAllFunnels(cross)
#convert the pedigree to a graph
pedigreeAsGraph <- pedigreeToGraph(pedigree)
#Plot it
plot(pedigreeAsGraph)
#Write it to a file in DOT format

mpMap2 documentation built on Sept. 13, 2020, 5:17 p.m.