qtlDesign (version 0.953)

Information: Information under null hypothesis of equal means

Description

Functions to calculate the information under the null hypothesis of no effect. Functions for discount factors for incomplete genotyping.

Usage

info(sel.frac,theta=0,cross)
info.bc(sel.frac,theta=0)
info.f2(sel.frac,theta=0)
deflate(theta,cross)
deflate.bc(theta)
deflate.f2(theta)
nullinfo(sel.frac)

Value

Information per individual for information functions, and the discount factor for the discount functions.

Arguments

cross

Cross type, either "bc" for backcross, or "f2" for intercross.

sel.frac

Selection fraction; proportion of extremes genotyped

theta

Recombination fraction between flanking markers

Author

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

Details

The nullinfo function calculates the information content per observation for any contrast between genotype means when densely genotyping an sel.frac fraction of the extreme phenotypic individuals. The information content is calculated under the null hypothesis of no difference between the genotype means. For small differences in genotype means, the information content will be approximately equal to the null, but in general, the information estimate under the null is the lower bound.

The info function calculates the information per observation for backcross, and F2 intercross under the null hypothesis of equal gentoype means. The information is calculated for a point in the middle of an interval spanned by markers separated by a recombination fraction theta. The function deflate calculates a deflation factor for the information attenuation in the middle of a marker interval relative to a completely typed location.

References

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

Examples

nullinfo(0.5)
info(0.5,cross="bc")
info(0.5,cross="f2")
info(0.5,0.1,cross="bc")
info(0.5,0.1,cross="f2")
deflate(0.1,"bc")
deflate(0.1,"f2")