Simulation of Chromosomal Regions Shared by Family Members
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Documentation for package ‘ibdsim2’ version 2.0.0
Help Pages
| convertPos | Conversion of genetic map positions |
| customMap | Custom recombination map |
| estimateCoeffs | Estimation of one- and two-locus relatedness coefficients |
| estimateIdentity | Estimation of one- and two-locus relatedness coefficients |
| estimateInbreeding | Estimation of one- and two-locus relatedness coefficients |
| estimateKappa | Estimation of one- and two-locus relatedness coefficients |
| estimateKinship | Estimation of one- and two-locus relatedness coefficients |
| estimateTwoLocusIdentity | Estimation of one- and two-locus relatedness coefficients |
| estimateTwoLocusInbreeding | Estimation of one- and two-locus relatedness coefficients |
| estimateTwoLocusKappa | Estimation of one- and two-locus relatedness coefficients |
| estimateTwoLocusKinship | Estimation of one- and two-locus relatedness coefficients |
| extractIds | Extract ID labels from simulation output |
| findPattern | Find specific IBD patterns |
| haploDraw | Draw haplotypes onto a pedigree plot |
| ibdsim | IBD simulation |
| karyoDiploid | Diploid karyogram |
| karyogram2 | Karyogram plots |
| karyoHaploid | Haploid karyogram |
| loadMap | Load a built-in genetic map |
| mapLen | Physical and genetic map lengths |
| mapLen.chromMap | Physical and genetic map lengths |
| mapLen.genomeMap | Physical and genetic map lengths |
| maplengths | Physical and genetic map lengths |
| physRange | Physical and genetic map lengths |
| physRange.chromMap | Physical and genetic map lengths |
| physRange.genomeMap | Physical and genetic map lengths |
| plotSegmentDistribution | Scatter plots of IBD segment distributions |
| profileSimIBD | Simulate markers conditional on a given IBD pattern |
| realised | Realised relatedness |
| realisedIdentity | Realised relatedness |
| realisedInbreeding | Realised relatedness |
| realisedKappa | Realised relatedness |
| realisedKinship | Realised relatedness |
| segmentStats | Summary statistics for identified segments |
| uniformMap | Uniform recombination maps |
| zeroIBD | Probability of zero IBD |