sim.mpped: Generate pedigrees from multi-parent designs

In mpMap: Multi-parent RIL genetic analysis

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

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.

Value

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

See Also

sim.mpcross

Examples

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

mpMap documentation built on May 29, 2017, 2:50 p.m.