This function simulates AFLP profiles (or other dominant markers) of parentals and several hybrid classes (F1 and backcrosses on both parentals). In addition, selection on several markers can be simulated for the hybrid progeny.
hybrid classes to simulate. By default 'all'. Also 'F1', 'BxA', 'BxB' or 'F2'.
Nsel
number of loci under selection.
S
Selection coefficient (see Details)
apa
value for parameter 1 of the beta distribution
apb
value for parameter 2 of the beta distribution
Details
Simulate dominant markers (AFLP, RFLP...). Parental allele frequencies are calculated following a beta distribution (Wright 1931).
F1, F2, Backcrosses to parental A (BxA) and Backcrosses to parental b (BxB) can be simulated with and without selection. The selection coefficient S is a integer value from -1 to ∞.This coefficient is 0 when there is no selection (similar to type = "neutral") and it varies following negative and positive directional selection (negative and positive values, respectively).
Balao, F. and GarcÃa-Castaño, J.L. AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations. Plant Methods10:40
Balao, F., Casimiro-Soriguer, R., GarcÃa-Castaño, J.L., Terrab, A., Talavera, S. 2013. Big thistle eats the little thistle: Non-neutral unidirectional introgression endangers the conservation of Onopordum hinojense. New Phytologist, in press.
Wright, S. 1931. Evolution in Mendelian Populations. Genetics16: 97-159.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(AFLPsim)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/AFLPsim/hybridsim.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hybridsim
> ### Title: AFLP simulator with selection
> ### Aliases: hybridsim
> ### Keywords: hybridization simulation
>
> ### ** Examples
>
> hybrids<-hybridsim(Nmarker=100, Na=30, Nb=30, Nf1=30, type="selection", S=10, Nsel=25, hybrid="F1")
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> dev.off()
null device
1
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