The genetics Package

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24 homozygote## [1] "withA" "withA" "rest" "withA" "rest" "withA" "rest" "rest" "rest"## [10] "rest" "rest" "rest" "rest" "rest" "rest" "rest"## --- Use of "*/*" ---map
homozygote 25Argumentsxgenotype object... optional parameters (ignored)allele.nameanyDetailsValuena.rmwhichcharacter value or vector of allele nameslogical value. When TRUE, a single count or indicator is returned by combiningthe results for all of the elements of allele. If FALSE separate counts orindicators should be returned for each element of allele. Defaults to FALSEif allele is missing. Otherwise defaults to TRUE.logical value indicating whether to remove missing values. When true, any NAvalues will be replaced by 0 or FALSE as appropriate. Defaults to FALSE.selects which allele to return. For first allele use 1. For second allele use 2. Forboth (the default) use c(1,2).When the allele.name argument is given, heterozygote and homozygote return TRUE if exactlyone or both alleles, respectively, match the specified allele.name.homozygote and heterozygotereturn a vector of logicals.carrier returns a logical vector if only one allele is specified, or if any is TRUE. Otherwise, itreturns matrix of logicals with one row for each element of allele.allele.count returns a vector of counts if only one allele is specified, or if any is TRUE.Otherwise, it returns matrix of counts with one row for each element of allele.allele returns a character vector when one allele is specified. When 2 alleles are specified, itreturns a 2 column character matrix.allele.names returns a character vector containing the set of allele names.Author(s)See AlsoGregory R. Warnes 〈warnes@bst.rochester.edu〉genotype, HWE.test, summary.genotype, locus gene markerExamplesexample.data
Page 1 and 2: The genetics PackageFebruary 16, 20
Page 3 and 4: HWE.exact 3See AlsoHWE.exact, HWE.t
Page 5 and 6: HWE.test 5## S3 method for class 'd
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: groupGenotype 23Examples## --- Setu
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

The genetics Package

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