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| cluster.pair | Computes pairwise similarity and clustering for a given pair of haplotypes for the currently selected chromosome. |
| clusthaplo | clusthaplo |
| config | Configure a clusthaplo context. |
| count.ancestral.alleles | Count ancestral alleles along a chromosome |
| generate.data | Simulated dataset generation |
| get.chromosome.names | Access to the list of chromosome names |
| get.config | Query the configuration of a clusthaplo context. |
| get.haplotypes.map | Access to the marker map of the haplotypes |
| get.kinship.matrix | Access to the kinship matrix |
| get.marker.data | Access to the marker data |
| get.mcqtl.consensus.map | Access to the MCQTL consensus marker map |
| get.scan.map | Access to the scan map used to compute the pairwise similarities |
| get.selected.chromosome | Access to the name of the currently selected chromosome |
| get.training.results | Access to the last training results |
| get.window.density | Access to the window density |
| MAP.SIZE.TOLERANCE | package constant: MAP.SIZE.TOLERANCE |
| MARKER.DOUBLE.EPSILON | package constant: MARKER.DOUBLE.EPSILON |
| pair.similarity | Computation of a pairwise similarity signal |
| pairwise.similarities | Computes pairwise similarity on all pairs of haplotypes for the currently selected chromosome. |
| parents.gen | Example dataset |
| parents.map | Example dataset |
| plot.clusthaplo.alleles | Graphic representation of the count of ancestral alleles along a chromosome |
| plot.clusthaplo.density | Graphic representation of the window density along a chromosome |
| plot.clusthaplo.haplotypes | Graphic representation of the clusterings along a chromosome |
| plot.clusthaplo.pair.similarity | Graphic representation of a single similarity signal along a chromosome |
| read.clusters | Read clustering data from a file |
| run | Runs the whole clusthaplo pipeline |
| run.equi.simulation | Run a simulation using the 'Equi' genotype simulator |
| run.mosaic.simulation | Run a simulation using the 'Mosaic' haplotype simulator |
| run.raw.simulation | Run a simulation without any post-processing |
| select.chromosome | Select a chromosome to operate on |
| set.debug | Debugging clusthaplo |
| set.verbose | Control verbosity of clusthaplo |
| train | Perform automated training of clusthaplo |
| transitive.closure | Performs transitive closure. |
| use.multicore | Enable parallelization |
| write.clusters | Output a clustering to file |
| write.xml | Output for MCQTL-LD |