homework(3) - STA 6178 Genetic Data Analysis Wu/Ma Homework...

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STA 6178 Genetic Data Analysis Wu/Ma Homework 3 (due February 24, 2005) Problem 1 – Investigation of the estimates from interval mapping Interval mapping constructed on the basis of mixture models has proven to be a powerful approach for mapping quantitative trait loci (QTL) that affect a quantitative trait. The statistical behavior of interval mapping can be investigated through simulation studies. Consider a backcross in which a linkage group of 6 equally distanced markers is constructed. The genetic distance between two adjacent markers is 20 cM. Assume that two QTL genotypes, Qq and qq, in the backcross have values μ 1 = 10 and μ 2 = 6, respectively. Given a QTL position, particular sample size and residual variance, one can simulate marker and phenotypic information. The simulated data are then analyzed by interval mapping to investigate how estimates of the parameters are consistent with given values. The parameters we need to estimate are = ( μ 1 , μ 2 , σ 2 , QTL location). In this problem, we design a few different cases. Using the software written by Dr. Ma, estimate the parameters, , and compare the consistency of parameter estimates and given values under the following cases: Case 1. Heritability = 0.1, sample size = 100, Case 2. Heritability = 0.1, sample size = 400, Case 3. Heritability = 0.4, sample size = 100, Case 4. Heritability = 0.4, sample size = 400 Note: Heritability is the ratio of genetic variance (
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homework(3) - STA 6178 Genetic Data Analysis Wu/Ma Homework...

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