rf_2pops: Multipoint recombination fraction based on two mapping...

Description Usage Arguments Value Note Author(s) References Examples

Description

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).

Usage

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

Arguments

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 3).

max.rf

maximum recombination fraction to declare linkage (defaults to 0.50).

log10.mintol

log base 10 of the minimum tolerance to converge the EM (defaults to -6)

max_it

maximum number of iteration to converge the EM (defaults to 50)

marker_names

an vector of strings with the marker order.

Value

A list with two objects of class rf_2pts, one for each population and the log-likelihood of the composite map

Note

The thresholds used for LOD and max.rf will be used in subsequent analyses, but can be overriden.

Author(s)

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

References

Quezada et al. 2018

Examples

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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)
}

rramadeu/onemap2pop documentation built on May 7, 2019, 9:23 p.m.