sim.mpped: Generate pedigrees from multi-parent designs

Description

Generates pedigrees for 4-way or 8-way MAGIC designs, with specifications given by the user. These pedigrees can be used to simulate datasets with other functions in the mpMap package.

Usage

sim.mpped(nfounders, nfunnels = 1, nperfam = 50, nssdgen = 6, nseeds = 1, iripgen = 0, seed = 1, ...)

Arguments

nfounders

Number of founders in the pedgiree

nfunnels

Number of different permutations of founder crosses (funnels) to generate.

nperfam

Number of plants per funnel (before selfing begins)

nssdgen

Number of generations of single-seed descent (selfing)

nseeds

Number of seeds propagated from each plant through SSD

iripgen

Number of generations of advanced intercrossing between mixing and selfing

seed

Random seed for selecting funnels to generate

...

Additional arguments

Value

Matrix with four columns: ID, mother, father, and observed status

Details

The 4-way pedigree is relatively simple compared to the 8-way pedigree, as there are many fewer possible combinations of lines to intercross. For a 4-way cross there is a maximum of 3 possible funnels (ABCD, ACBD and ADBC), while there are 315 for an 8-way cross. This is computed under the assumption that cross AB is equivalent to cross BA.

For a value of 1, the funnel will be of the form ABCD or ABCDEFGH. For values less than the maximum possible number of funnels the crosses will be selected randomly, with each possibly funnel having equal probability of being generated.

Examples

Run this code

ped4way <- sim.mpped(4, 1, 500, 6, 1)
ped8way <- sim.mpped(8, 1, 500, 6, 1)