detailedPedigree-class: Pedigree for simulation
In mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description Usage Arguments Value Functions Slots See Also Examples

Class detailedPedigree is similar to the S4 class pedigree, except it also contains information about which lines are going to observed. This allows simulation of a data set with the given pedigree.

1	detailedPedigree(lineNames, mother, father, initial, observed, selfing)

`lineNames`	The names assigned to the lines.
`mother`	The female parent of this line, given by name or by index within `lineNames`.
`father`	The male parent of this line, given by name or by index within `lineNames`.
`initial`	The founder lines, given by name or by index within lineNames.
`observed`	The lines which are observed in the final population, given by name or by index within lineNames.
`selfing`	Value determining whether or not subsequent analysis of populations generated from this pedigree should assume infinite generations of selfing. Possible values are `"finite"` and `"infinite"`.

An object of class detailedPedigree, suitable for simulation.

detailedPedigree: Construct object of class detailedPedigree

initial: The indices of the inbred founder lines in the pedigree. These founders lines must be the first lines in the pedigree.
observed: A logical vector with one value per line in the pedigree. A value of TRUE indicates that this line will be genotyped.

pedigree-class, simulateMPCross, detailedPedigree

detailedPedigree-class

lineNames <- paste0("L", 1:10)
mother <- c(0, 0, 1, rep(3, 7))
father <- c(0, 0, 2, rep(2, 7))
initial <- 1:2
lineNames <- paste0("L", 1:10)
observed <- c(rep(FALSE, 3), rep(TRUE, 7))
detailedPedigreeObj <- detailedPedigree(mother = mother, father = father, initial = initial, 
	observed = observed, lineNames = lineNames, selfing = "finite")