ripple_2pops: Compares and displays plausible alternative orders for a...

Description Usage Arguments Details Value Author(s) References Examples

Description

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.

Usage

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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)

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.

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 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)

window

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

marker_names

an vector of strings with the marker order.

Details

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

Value

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

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]
#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)
}

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