Sample of n = 230 genotype counts discussed in Lauretto et al. (2009, Example 3). These data come from a rheumatoid arthritis (RA) study performed by Wordsworth et al. (1992), where two hundred and thirty RA patients were genotyped for the HLA-DR locus. The DR4 allele was subdivided into Dw4, Dw14 and other subtypes. DRX represents all non-DR1, non-Dw4, non-Dw14 alleles.
An object of class
Lauretto, M.S., Nakano, F., Faria, S.R., Pereira, C.A.B. and Stern, J.M. (2009), "A straightforward multiallelic significance test for the Hardy-Weinberg equilibrium law". Genetics and Molecular Biology, Vol. 32, No. 3, 619–625.
Consonni, G., Moreno, E., and Venturini, S. (2011). "Testing Hardy-Weinberg equilibrium: an objective Bayesian analysis". Statistics in Medicine, 30, 62–74. http://onlinelibrary.wiley.com/doi/10.1002/sim.4084/abstract Wordsworth, P., Pile, K.D., Buckley, J.D., Lanchbury, J.S.S., Ollier, B., Lathrop, M. and Bell, J.I. (1992), "HLA heterozygosity contributes to susceptibility to rheumatoid arthritis". American Journal of Human Genetics, 51, 3, 585–591.
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# Example 1 # ## Not run: # ATTENTION: the following code may take a long time to run! # data(Wordsworth) plot(Wordsworth) n <- sum(Wordsworth@data.vec, na.rm = TRUE) out <- hwe.ibf.mc(Wordsworth, t = n/2, M = 100000, verbose = TRUE) summary(out, plot = TRUE) ## End(Not run) # Example 2 # ## Not run: # ATTENTION: the following code may take a long time to run! # data(Wordsworth) n <- sum(Wordsworth@data.vec, na.rm = TRUE) M <- 300000 f <- seq(.1, 1, .05) out <- hwe.ibf.plot(y = Wordsworth, t.vec = round(f*n), M = M) ## End(Not run)
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