optspacing: Optimal marker spacing

In qtlDesign: Design of QTL Experiments

Optimal marker spacing

Description

Functions to find optimal marker spacing given cost.

Usage

optspacing(cost,G=NULL,sel.frac,cross)
optspacing.bc(cost,G=NULL,sel.frac)
optspacing.f2(cost,G=NULL,sel.frac)
optspacing(cost,G=NULL,sel.frac=NULL,cross)
optspacing.bc(cost,G=NULL,sel.frac=NULL)
optspacing.f2(cost,G=NULL,sel.frac=NULL)

Arguments

cost	Cost of genotyping in units of raising an individual
sel.frac	Selection fraction; proportion of individuals genotyped
G	Genome size in centiMorgans
cross	Cross type, "bc" or "f2"

Details

The function optim is used to search for the optima.

Value

In the first form, with the selection fraction specified, the spacing in centiMorgans that maximizes the information to cost ratio in the middle of the marker interval. In the second form, with the selection fraction unspecified, it returns the value of (spacing,sel.frac) which maximizes the information to cost ratio in the middle of the marker interval.

Author(s)

Saunak Sen, Jaya Satagopan, Karl Broman, and Gary Churchill

References

Sen S, Satagopan JM, Churchill GA (2005) Quantitative trait locus study design from an information perspective. Genetics, 170:447-64.

See Also

optim, optimize

Examples

optspacing(cost=0.1,G=1440,sel.frac=0.5,cross="bc")
optspacing(cost=30/3000,G=1440,sel.frac=NULL,cross="f2")

qtlDesign documentation built on March 21, 2024, 3:01 a.m.