Description Usage Arguments Details Value Author(s) References See Also Examples
Provides expected confidence interval widths for QTL location when we have dense markers.
1  ci.length(cross,n,effect,p=0.95,sigma2=1,env.var,gen.var,bio.reps=1)

cross 
String indicating cross type which is "bc", for backcross, "f2" for intercross, and "ri" for recombinant inbred lines. 
n 
Sample size 
p 
Confidence level for desired confidence interval 
effect 
The QTL effect we want to detect. For

sigma2 
Error variance; if this argument is absent,

env.var 
Environmental (within genotype) variance 
gen.var 
Genetic (between genotype) variance due to all loci segregating between the parental lines. 
bio.reps 
Number of biological replicates per unique genotype. This is usually 1 for backcross and intercross, but may be larger for RI lines. 
With dense markers, the log likelihood follows a compound process. Approximate expected confidence intervals can be calculated by pretending the log likelihood decays linearly with a drift rate that depends on the effect size and cross type.
Returns the expected confidence interval width in cM assuming dense markers.
Saunak Sen
Dupuis J and Siegmund D (1999) Statistical methods for mapping quantitative trait loci from a dense set of markers. Genetics 151:373386.
Darvasi A (1998) Experimental strategies for the genetic dissection of complex traits in animal models. Nature Genetics 18:1924.
Kong A and Wright FA (1994) Asymptotic theory for gene mapping. Proceedings of the National Academy of Sciences of the USA 91:97059709.
1  ci.length(cross="bc",n=400,effect=5,p=0.95,sigma2=1)

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