Description Usage Arguments Value Note Author(s) References Examples

The function 'rf_2pops' estimates the recombination fraction based on two mapping populations. It estimates the recombination fractions based on a multipoint approach implemented using the methodology of Hidden Markov Models (HMM) with the Expectation Maximization (EM) algorithm as explained in the supplementary material of Quezada et al. (2017).

1 2 | ```
rf_2pops(markers_names, data_P1, data_P2, rftwopoints_P1, rftwopoints_P2,
LOD = 3, max.rf = 0.5, log10.mintol = -6, max_it = 50)
``` |

`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. |

`rftwopoints_P1` |
an rf_2pts object with the information of rf from the first population. |

`rftwopoints_P2` |
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 |

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

A list with two objects of class `rf_2pts`

, one for each population and the
log-likelihood of the composite map

The thresholds used for `LOD`

and `max.rf`

will be used in
subsequent analyses, but can be overriden.

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 | ```
notrun{
data(onemap2pop)
#Extracting the marker names:
order_LG1POP1 <- colnames(POP1.geno$geno)[LG1_POP1_final$seq.num]
#Computing the rf and likelihood considering information of POP1 and POP2
LG1_POP1order <- rf_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 = 60)
}
``` |

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.