Information under null {qtlDesign}R Documentation

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.null(alpha)
info.bc.null(alpha,theta=0)
info.f2.null(alpha,theta=0)
deflate.bc(theta)
deflate.f2(theta)

Arguments

alpha Selection fraction; proportion of extremes genotyped
theta Recombination fraction between flanking markers

Details

The info.null function calculates the information content per observation for any contrast between genotype means when densely genotyping an alpha 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.bc.null and info.f2.null functions calculate the information per observation for backcross, and F2 intercross respectively 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.

Value

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

Note

Only functions for backcross available right now.

Author(s)

Saunak Sen, Jaya Satagopan, and Gary Churchill

References

Sen, Satagopan, and Churchill (2004), QTL study design from an information perspective, http://repositories.cdlib.org/cbmb/QTLdesign.

See Also

info2cost.bc.null

Examples

info.null(0.5)
info.bc.null(0.5)
info.f2.null(0.5)
info.bc.null(0.5,0.1)
info.f2.null(0.5,0.1)
deflate.bc(0.1)
deflate.f2(0.1)

[Package qtlDesign version 0.32 Index]