Description Usage Arguments Details Value Author(s) Examples

Input is genotype data.

Can handle all genotype data with multialleles and is thus not restricted to SNP data.

1 | ```
geno.setup(G,returnNames=TRUE,haplo.baseline=NULL)
``` |

`G` |
genotype data, n rows with 2*p columns. |

`returnNames` |
return names of haplotype. |

`haplo.baseline` |
gives the name of the haplotype that should be used as baseline, for latter MLE fitting. Default is last haplotype. |

This function provides an efficient representation of haplotypes that are consistent with genotype data. This speeds up the calculation of the likelihood of the genotype data, given the frequencies of haplotypes.

The component `out$HPIordered`

returned contains the most important
information. `out$HPIordered`

is list, with one entry per
person. `out$HPIordered[[i]]`

is a list, with one entry per
haplotype pair consistent with the genotype data
`out$HPIordered[[i]][[j]]`

is a vector of two integers, which are
the indices of the `j`

th pair of haplotypes consistent with the
genotypes for
individual `i`

. The haplotypes that these indices correspond to
can be examined by looking at

`out$uniqueHaploNames[out$HPIordered[[i]][[j]]]`

.

Returns an object of class `geno.setup`

with the following arguments:

`HPIordered` |
list of indices of haplotype pairs that can lead to the observed genotype |

`uniqueHaploNames` |
names of haplotypes, with alleles separated by columns. This list includes only haplotypes which are consistent with the genotypes for individuals in the sample. |

`nAllelesPerLocus` |
number of alleles for each locus. |

`unorderedAlleles` |
A list, with one component corresponding to a locus, and this component is a vector of the allele names found at this locus. |

`nPeople` |
number of subjects. |

`nPossHaps` |
A vector of the number of possible haplotype pairs for each subject. |

`nLoci` |
number of loci. |

`initial.freqs` |
simple estimator of haplotype frequencies, based on simply counting the occurrences of each haplotype relative to the total number of possible haplotypes for all subjects. |

Jeremy Silver

1 2 3 4 5 6 7 | ```
n<-10
g<-matrix(rbinom(10*4,1,0.5),n,4); # simple genotypes
gs<-geno.setup(g);
summary(gs);
gs
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.