The genetics Package

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26 locuscarrier(g1,"D")carrier(g1,"D",na.rm=TRUE)# get count of one alleleallele.count(g1,"D")# get count of each alleleallele.count(g1) # equivalent toallele.count(g1, c("D","I"), any=FALSE)# get combined count for both allelesallele.count(g1,c("I","D"))# get second alleleallele(g1,2)# get both allelesallele(g1)locusCreate and Manipulate Locus, Gene, and Marker ObjectsDescriptionUsagelocus, gene, and marker create objects to store information, respectively, about genetic loci,genes, and markers.is.locus, is.gene, and ismarker test whether an object is a member of the respective class.as.character.locus, as.character.gene, as.character.marker return a characterstring containing a compact encoding the object.getlocus, getgene, getmarker extract locus data (if present) from another object.locus
locus 27is.marker(x)## S3 method for class 'locus':as.character(x, ...)## S3 method for class 'gene':as.character(x, ...)## S3 method for class 'marker':as.character(x, ...)getlocus(x, ...)locus(x)
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 and 24: groupGenotype 23Examples## --- Setu
Page 25: homozygote 25Argumentsxgenotype obj
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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