Optimal marker spacing {qtlDesign} | R Documentation |
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
Examples
optspacing(cost=0.1,G=1440,sel.frac=0.5,cross="bc")
optspacing(cost=30/3000,G=1440,sel.frac=NULL,cross="f2")