twoParentPedigree: Generate a two-parent pedigree which starts from inbred...

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

Description

Generate a two-parent pedigree starting from inbred founders

Usage

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

Arguments

initialPopulationSize	The number of F1 lines generated
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 F1 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.

Examples

plotWOptions <- function(graph) 
	plot(graph, vertex.size = 8, vertex.label.cex=0.6, edge.arrow.size=0.01, edge.width=0.2)
#F2 design
pedigree <- twoParentPedigree(initialPopulationSize = 10, selfingGenerations = 1, 
	intercrossingGenerations = 0, nSeeds = 1)
graph <- pedigreeToGraph(pedigree)
plotWOptions(graph)

#An equivalent F2 design (if the founders really are inbred)
pedigree <- twoParentPedigree(initialPopulationSize = 10, selfingGenerations = 0, 
	intercrossingGenerations = 1, nSeeds = 0)
graph <- pedigreeToGraph(pedigree)
plotWOptions(graph)

#Another equivalent F2 design (if the founders really are inbred)
pedigree <- twoParentPedigree(initialPopulationSize = 1, selfingGenerations = 1, 
	intercrossingGenerations = 0, nSeeds=10)
graph <- pedigreeToGraph(pedigree)
plotWOptions(graph)

#A RIL design (10 generations of inbreeding)
pedigree <- twoParentPedigree(initialPopulationSize = 10, selfingGenerations = 10, 
	intercrossingGenerations = 0, nSeeds = 1)
graph <- pedigreeToGraph(pedigree)
plotWOptions(graph)

#Another RIL design (10 generations of inbreeding)
pedigree <- twoParentPedigree(initialPopulationSize = 1, selfingGenerations = 10, 
	intercrossingGenerations = 0, nSeeds = 10)
graph <- pedigreeToGraph(pedigree)
plotWOptions(graph)
#One generation of mixing followed by 10 generations of inbreeding
pedigree <- twoParentPedigree(initialPopulationSize = 10, selfingGenerations = 10, 
	intercrossingGenerations = 1, nSeeds = 1)
graph <- pedigreeToGraph(pedigree)
plotWOptions(graph)

#Two generations of mixing and no inbreeding
pedigree <- twoParentPedigree(initialPopulationSize = 10, selfingGenerations = 0, 
	intercrossingGenerations = 2, nSeeds = 0)
graph <- pedigreeToGraph(pedigree)
plotWOptions(graph)

#One generation of mixing, and then two selfed lines are generated (10 generations of selfing)
pedigree <- twoParentPedigree(initialPopulationSize = 10, selfingGenerations = 10, 
	intercrossingGenerations = 1, nSeeds = 2)
graph <- pedigreeToGraph(pedigree)
plotWOptions(graph)

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