R/qtlDesign: inbred line cross experimental design.
Document Type
Article
Publication Date
2007
Keywords
Animals-Inbred-Strains, Chromosome-Mapping, Crosses-Genetic, Probability, Quantitative-Trait-Loci, Variation-(Genetics)
First Page
87
Last Page
93
JAX Source
Mamm Genome 2007 Feb; 18(2):87-93.
Abstract
An investigator planning a QTL (quantitative trait locus) experiment has to choose which strains to cross, the type of cross, genotyping strategies, and the number of progeny to raise and phenotype. To help make such choices, we have developed an interactive program for power and sample size calculations for QTL experiments, R/qtlDesign. Our software includes support for selective genotyping strategies, variable marker spacing, and tools to optimize information content subject to cost constraints for backcross, intercross, and recombinant inbred lines from two parental strains. We review the impact of experimental design choices on the variance attributable to a segregating locus, the residual error variance, and the effective sample size. We give examples of software usage in real-life settings. The software is available at http://www.biostat.ucsf.edu/sen/software.html .
Recommended Citation
Sen S,
Satagopan JM,
Broman KW,
Churchill GA.
R/qtlDesign: inbred line cross experimental design. Mamm Genome 2007 Feb; 18(2):87-93.