mpMap2 (version 1.0.4)

detailedPedigree-class: Pedigree for simulation

Description

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.

Usage

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

Arguments

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".

Value

An object of class detailedPedigree, suitable for simulation.

Functions

• detailedPedigree: Construct object of class detailedPedigree

Slots

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.

See Also

pedigree-class, simulateMPCross, detailedPedigree

detailedPedigree-class

Examples

# NOT RUN {
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")
# }