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Mamm Genome. 2007 Feb;18(2):87-93. Epub 2007 Mar 8.

R/qtlDesign: inbred line cross experimental design.

Author information

1
Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA. sen@biostat.ucsf.edu

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 .

PMID:
17347894
PMCID:
PMC2366108
DOI:
10.1007/s00335-006-0090-y
[Indexed for MEDLINE]
Free PMC Article

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