Description Usage Arguments Value Examples
View source: R/twoParentPedigree.R
Generate a two-parent pedigree starting from inbred founders
1 2 3 4 5 6 | twoParentPedigree(
initialPopulationSize,
selfingGenerations,
nSeeds = 1L,
intercrossingGenerations
)
|
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 |
An object of class detailedPedigree
representing the experimental design, suitable for simulation using simulateMPCross.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.