Description Usage Arguments Details Value Author(s) References Examples

For a given sequence of ordered markers, computes the multipoint likelihood
of alternative orders, by shuffling subsets (windows) of markers within the
sequence. For each position of the window, all possible *(ws)!*
orders are compared.

1 2 3 | ```
ripple_2pops(markers_names, data_P1, data_P2, twopts_POP1, twopts_POP2,
LOD = 3, max.rf = 0.5, log10.mintol = -6, max_it = 50,
window = 3)
``` |

`data_P1` |
an onemap object class with the information of the first population. |

`data_P2` |
an onemap object class with the information of the second population. |

`twopts_POP1` |
an rf_2pts object with the information of rf from the first population. |

`twopts_POP2` |
an rf_2pts object with the information of rf from the second population. |

`LOD` |
minimum LOD Score to declare linkage (defaults to |

`max.rf` |
maximum recombination fraction to declare linkage (defaults
to |

`log10.mintol` |
log base 10 of the minimum tolerance to converge the EM (defaults to |

`max_it` |
maximum number of iteration to converge the EM (defaults to |

`window` |
an integer specifying the length of the window size (defaults to 4). |

`marker_names` |
an vector of strings with the marker order. |

Large values for the window size make computations very slow, specially if there are many partially informative markers.

A list with two objects. The first is a matrix with the tested ordered markers, the second is a vector with the respectivally log-likelihood

Rodrigo R Amadeu [email protected] and Marianella Quezada [email protected]

Quezada et al. 2018

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ```
notrun{
data(onemap2pop)
#Extracting the marker names:
order_LG1POP1 <- colnames(POP1.geno$geno)[LG1_POP1_final$seq.num]
#RIPPLE algorithm:
LG1_POP1order <- ripple_2pops(markers_names = order_LG1POP1,
data_P1 = POP1_geno,
data_P2 = POP2_geno,
rftwopoints_P1 = twopts_POP1,
rftwopoints_P2 = twopts_POP2,
LOD = 3,
max.rf = 0.5,
log10.mintol = -6,
max_it = 50,
window = 4)
}
``` |

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