AFLP simulator with selection from parental data

Description

This function simulates AFLP profiles (or other dominant markers) of several hybrid classes (F1 and backcrosses on both parentals) from two parental populations. In addition, selection on several markers can be simulated for the hybrid progeny.

Usage

hybridize(pa,pb,Nf1, Nbxa = Nf1, Nbxb = Nf1, Nf2 = Nf1, type = "selection",
 hybrid = "all", Nsel = Nmarker * 0.1, S = 0)

Arguments

Details

simulates F1, F2, Backcross to Parental A (BxA) and Backcross to Parental B (BxB) with and without selection. Parental profiles must be included (individuals in rows and markers in columns). he 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).

Value

Object hybridsim with:

Author(s)

F. Balao fbalao@us.es, J.L. García-Castaño

References

Balao, F. and García-Castaño, J.L. AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations. Plant Methods 10:40

Balao, F., Casimiro-Soriguer, R., García-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. Genetics 16: 97-159.

See Also

hybridsim

Examples

## AFLP profile Species A
SpeciesA<-read.table(system.file("/files/SpeciesA.txt",package="AFLPsim"),header=TRUE, row.names=1)


## AFLP profile Species B
SpeciesB<-read.table(system.file("/files/SpeciesB.txt",package="AFLPsim"),header=TRUE, row.names=1)

## simulate F1 hybrids
F1hybrids<-hybridize(pa=SpeciesA,pb=SpeciesB, Nf1=30, type="neutral", hybrid="F1")

Results

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/hybridize.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hybridize
> ### Title: AFLP simulator with selection from parental data
> ### Aliases: hybridize
> ### Keywords: hybridization simulation
> 
> ### ** Examples
> 
> ## AFLP profile Species A
> SpeciesA<-read.table(system.file("/files/SpeciesA.txt",package="AFLPsim"),header=TRUE, row.names=1)
> 
> 
> ## AFLP profile Species B
> SpeciesB<-read.table(system.file("/files/SpeciesB.txt",package="AFLPsim"),header=TRUE, row.names=1)
> 
> ## simulate F1 hybrids
> F1hybrids<-hybridize(pa=SpeciesA,pb=SpeciesB, Nf1=30, type="neutral", hybrid="F1")
########Neutral hybridization########> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>