Information under null {qtlDesign} | R Documentation |
Functions to calculate the information under the null hypothesis of no effect. Functions for discount factors for incomplete genotyping.
info.null(alpha) info.bc.null(alpha,theta=0) info.f2.null(alpha,theta=0) deflate.bc(theta) deflate.f2(theta)
alpha |
Selection fraction; proportion of extremes genotyped |
theta |
Recombination fraction between flanking markers |
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
.
Information per individual for information functions, and the discount factor for the discount functions.
Only functions for backcross available right now.
Saunak Sen, Jaya Satagopan, and Gary Churchill
Sen, Satagopan, and Churchill (2004), QTL study design from an information perspective, http://repositories.cdlib.org/cbmb/QTLdesign.
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)