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1、The genetics Package August 21, 2008 Title Population Genetics Version 1.3.4 Date 2008-08-20 Author Gregory Warnes, with contributions from Gregor Gorjanc, Friedrich Leisch, and Michael Man. Maintainer Gregory Warnes Depends combinat, gdata, gtools, MASS, mvtnorm Description Classes and methods for
2、handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, fl agging homo/heterozygotes, fl agging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequil
3、ibrium, estimating and testing for linkage disequilibrium, . biocViews Genetics License GPL R topics documented: HWE.chisq. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2 HWE.exact. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3 HWE
4、.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4 LD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6 ci.balance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9 Depreciated . . .
5、 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10 diseq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11 expectedGenotypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14 genotype . . . . . . . . . .
6、. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15 gregorius. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20 groupGenotype . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22 homozygote . . . . . . . . . . . . . . . .
7、. . . . . . . . . . . . . . . . . . . . . . . . .24 locus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26 makeGenotypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30 1 2HWE.chisq order.genotype. . . . . . . . . . . . . . .
8、 . . . . . . . . . . . . . . . . . . . . . . . .32 plot.genotype . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35 print.LD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36 summary.genotype. . . . . . . . . . . . . . . . . . . .
9、. . . . . . . . . . . . . . . . .38 undocumented . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40 write.pop.fi le. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40 Index42 HWE.chisqPerform Chi-Square Test for Hardy-Weinberg Equilibrium
10、Description Test the null hypothesis that Hardy-Weinberg equilibrium holds using the Chi-Square method. Usage HWE.chisq(x, .) # S3 method for class genotype: HWE.chisq(x, simulate.p.value=TRUE, B=10000, .) Arguments xgenotype or haplotype object. simulate.p.value a logical value indicating whether t
11、he p-value should be computed using simu- lation instead of using the 2approximation. Defaults to TRUE. BNumber of simulation iterations to use when simulate.p.value=TRUE. Defaults to 10000. .optional parameters passed to chisq.test Details This function generates a 2-way table of allele counts, the
12、n calls chisq.test to compute a p- value for Hardy-Weinberg Equilibrium. By default, it uses an unadjusted Chi-Square test statistic andcomputesthep-valueusingasimulation/permutationmethod. Whensimulate.p.value=FALSE, it computes the test statistic using the Yates continuity correction and tests it
13、against the asymptotic Chi-Square distribution with the approproate degrees of freedom. Note: The Yates continuty correction is applied *only* when simulate.p.value=FALSE, so thatthereportedteststatisticswhensimulate.p.value=FALSEandsimulate.p.value=TRUE will differ. Value An object of class htest.
14、HWE.exact3 See Also HWE.exact, HWE.test, diseq, diseq.ci, allele, chisq.test, boot, bootci Examples example.data 0: Dmax= minpipj,pjpi= pipj or if D 0: Dmax= minpi(1 pj),pj(1 pi) r is the correlation coeffi cient between two alleles, and can be computed by r = D p(p i (1 pi)p(j)(1 pj) where - pi def
15、i ned as the observed probability of allele i, - pj defi ned as the observed probability of allele j, and - pij defi ned as the observed probability of the allele pair ij. When there are more than two alleles, the summary values for these statistics are obtained by com- puting a weighted average of
16、the absolute value of each allele pair, where the weight is determined by the expected frequency. For example: Doverall= X i6=j |Dij| pij Bootstrapping is used to generate confi dence interval in order to avoid reliance on parametric as- sumptions, which will not hold for alleles with low frequencies (e.g. D0following a a Chi-square distribution). See the function HWE.test for testing Hardy-Weinberg Equilibrium, D = 0. diseq13 Value diseq returns an object of class diseq w
