The genetics Package

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4 HWE.testNoteThis function only works for genotypes with exactly 2 alleles.Author(s)David Duffy 〈davidD@qimr.edu.au〉 with modifications by Gregory R. Warnes 〈warnes@bst.rochester.edu〉ReferencesEmigh TH. (1980) "Comparison of tests for Hardy-Weinberg Equilibrium", Biometrics, 36, 627-642.See AlsoHWE.chisq, HWE.test, diseq, diseq.ciExamplesexample.data
HWE.test 5## S3 method for class 'data.frame':HWE.test(x, ..., do.Allele.Freq=TRUE, do.HWE.test=TRUE)## S3 method for class 'HWE.test':print(x, show=c("D","D'","r","table"), ...)Argumentsxgenotype or haplotype object.exact a logical value indicated whether the p-value should be computed using the exactmethod, which is only available for 2 allele genotypes.simulate.p.valuea logical value indicating whether the p-value should be computed using simulationinstead of using the χ 2 approximation. Defaults to TRUE.BDetailsValueconfci.BshowNumber of simulation iterations to use when simulate.p.value=TRUE.Defaults to 10000.Confidence level to use when computing the confidence level for D-hat. Defaultsto 0.95, should be in (0,1).Number of bootstrap iterations to use when computing the confidence interval.Defaults to 1000.a character vector containing the names of HWE test statistics to display fromthe set of "D", "D’", "r", and "table".... optional parameters passed to HWE.test (data.frame method) or chisq.test(base method).do.Allele.Freqlogicial indication whether to summarize allele frequencies.do.HWE.testlogicial indication whether to perform HWE testsHWE.test calls diseq to computes the Hardy-Weinberg (dis)equilibrium statistics D, D’, and r(correlation coefficient). Next it calls diseq.ci to compute a bootstrap confidence interval forthese estimates. Finally, it calls chisq.test to compute a p-value for Hardy-Weinberg Equilibriumusing a simulation/permutation method.Using bootstrapping for the confidence interval and simulation for the p-value avoids reliance on theassumptions the underlying Chi-square approximation. This is particularly important when someallele pairs have small counts.For details on the definition of D, D’, and r, see the help page for diseq.An object of class HWE.test with componentsdiseqcitestA diseq object providing details on the disequilibrium estimates.A diseq.ci object providing details on the bootstrap confidence intervals forthe disequilibrium estimates.A htest object providing details on the permutation based Chi-square test.
Page 1 and 2: The genetics PackageFebruary 16, 20
Page 3: HWE.exact 3See AlsoHWE.exact, HWE.t
Page 7 and 8: LD 7UsageLD(g1, ...)## S3 method fo
Page 9 and 10: ci.balance 9# Compute LD table for
Page 11 and 12: diseq 11Usagediseq(x, ...)## S3 met
Page 13 and 14: expectedGenotypes 13Examplesexample
Page 15 and 16: genotype 15DescriptionUsagegenotype
Page 17 and 18: genotype 17that appear in the data,
Page 19 and 20: genotype 19m4
Page 21 and 22: groupGenotype 21retval$missprobComp
Page 23 and 24: groupGenotype 23Examples## --- Setu
Page 25 and 26: homozygote 25Argumentsxgenotype obj
Page 27 and 28: locus 27is.marker(x)## S3 method fo
Page 29 and 30: makeGenotypes 29example.data
Page 31 and 32: makeGenotypes 31test1replace=TRUE),
Page 33 and 34: order.genotype 33ValueThe same as i
Page 35 and 36: power.casectrl 35See Alsogenotype,
Page 37 and 38: print.LD 37print.LDTextual and grap
Page 39 and 40: summary.genotype 39data
Page 41 and 42: undocumented 41Examplesexample.data
Page 43 and 44: Index∗Topic IOwrite.pop.file, 41
Page 45: INDEX 45write.marker.file(write.pop

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