The genetics Package

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30 makeGenotypesDetailsValueThe functions makeGenotypes and makeHaplotypes allow the conversion of all of the genetic variablesin a dataset to genotypes or haplotypes in a single step.The parameter convert may be missing, a vector of column names, indexes or true/false indictators,or a list of column name or index pairs.When the argument convert is not provided, the function will look for columns where at leasttol*100% of the records contain the separator character sep (’/’ by default). These columns willthen be assumed to contain both of the genotype/haplotype alleles and will be converted in-place togenotype variables.When the argument convert is a vector of column names, indexes or true/false indictators, thecorresponding columns will be assumed to contain both of the genotype/haplotype alleles and willbe converted in-place to genotype variables.When the argument convert is a list containing column name or index pairs, the two elementsof each pair will be assumed to contain the individual alleles of a genotype/haplotype. The firstcolumn specified in each pair will be replaced with the new genotype/haplotype variable namedname1 + sep + name2. The second column will be removed.Note that the method argument may be used to supply a non-standard conversion function, suchas as.genotype.allele.count, which converts from [0,1,2] to [’A/A’,’A/B’,’A/C’] (or thespecified allele names). See the example below.All other variables will be un-Dataframe containing converted genotype/haplotype variables.changed.Author(s)Gregory R. Warnes 〈warnes@bst.rochester.edu 〉See AlsogenotypeExamples## Not run:# common casedata
makeGenotypes 31test1replace=TRUE),sample(c("134","138","140","142","146"),20,replace=TRUE),sep=" / "),G3=sample(c("A /T","T /T","T /A"),20, replace=TRUE),comment=sample(c("Possible Bad Data/Lab Error",""),20,rep=TRUE))# now automatically convert genotype columnsgeno1
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 and 26: homozygote 25Argumentsxgenotype obj
Page 27 and 28: locus 27is.marker(x)## S3 method fo
Page 29: makeGenotypes 29example.data
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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