info: Information under null hypothesis of equal means

In qtlDesign: Design of QTL experiments

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)

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

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.

Value

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

Note

Information is calculated under the equal means assumption. This approximation is very good in practice, and is slightly conservative. If the difference between the means is large, these functions will underestimate the information. For power calculations, that is okay.

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.

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")

qtlDesign documentation built on May 2, 2019, 5:21 a.m.