The genetics Package

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6 LDcallfunction call used to creat this object.conf, B, ci.B, simulate.p.valuevalues used for these arguments.Author(s)Gregory R. Warnes 〈warnes@bst.rochester.edu 〉See Alsogenotype, diseq, diseq.ci, HWE.chisq, HWE.exact,Examplesexample.data
LD 7UsageLD(g1, ...)## S3 method for class 'genotype':LD(g1,g2,...)## S3 method for class 'data.frame':LD(g1,...)Argumentsg1g2Detailsgenotype object or dataframe containing genotype objectsgenotype object (ignored if g1 is a dataframe)... optional arguments (ignored)Linkage disequilibrium (LD) is the non-random association of marker alleles and can arise frommarker proximity or from selection bias.LD.genotype estimates the extent of LD for a single pair of genotypes. LD.data.frame computesLD for all pairs of genotypes contained in a data frame. Before starting, LD.data.framechecks the class and number of alleles of each variable in the dataframe. If the data frame containsnon-genotype objects or genotypes with more or less than 2 alleles, these will be omitted from thecomputation and a warning will be generated.Three estimators of LD are computed:D raw difference in frequency between the observed number of AB pairs and the expected number:D = p AB − p A p BD’ scaled D spanning the range [-1,1]D ′ =DD maxwhere, if D > 0:or if D < 0:D max = min(p A p b , p a p B )D max = max −p A p B , −p a p br correlation coefficient between the markersr =−D√(pA ∗ p a ∗ p B ∗ p b )where- p A is defined as the observed probability of allele ’A’ for marker 1,- p a = 1 − p A is defined as the observed probability of allele ’a’ for marker 1,
Page 1 and 2: The genetics PackageFebruary 16, 20
Page 3 and 4: HWE.exact 3See AlsoHWE.exact, HWE.t
Page 5: HWE.test 5## S3 method for class 'd
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

The genetics Package

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