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Last data update: 2014.03.03

R: Identifying candidate loci under natural selection with...

bayescan

R Documentation

Identifying candidate loci under natural selection with external application

Description

This function calls Bayescan program from within R to identifying candidate loci under natural selection from genetic data.

Usage

bayescan(mat, filename, nbp = 20, pilot = 5000, burn = 50000, exec=NULL)

Arguments

`mat`	A matrix with genotypic data to test in hybridsim format
`filename`	a character string giving the name of the output file (without extension)
`nbp`	Number of pilot runs (default is 2)
`pilot`	Length of pilot runs (default is 50)
`burn`	Burnin length (default is 5000)
`exec`	a character string giving the path to BAYESCAN. By default it tries to guess it depending on the operating system (see details).

Details

bayescan tries to guess the name of the executable program depending on the operating system. Specifically, the followings are used: "bayescan_2.1" under Linux and Mac, or "C:/Program Files/BayeScan2.1/binaries/BayeScan2.1_win32bits_cmd_line.exe" under Windows.

Value

Several files with the results and a data.frame with the following variables:

`prob`	The posterior probability for the model including selection
`log10.PO.`	The logarithm of Posterior Odds to base 10
`qval`	q-values for each locus for the model including selection
`alpha`	The estimated alpha coefficient indicating the strength and direction of selection. See Bayescan 2.1 manual
`fst`	The Fst coefficient averaged over populations

Author(s)

F. Balao fbalao@us.es, J.L. GarcÃa-CastaÃ±o

References

Foll, M. & O. Gaggiotti. 2008. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180: 977-993.

Examples

## Not run
hybrids<-hybridsim(Nmarker=100, Na=30, Nb=30, Nf1=30, type="selection", Nsel=25, hybrid="F1", S=100)
outbayes<-bayescan(hybrids, filename="bayescanresults", nbp=10, pilot=50, burn=100)
outbayes

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/bayescan.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bayescan
> ### Title: Identifying candidate loci under natural selection with external
> ###   application
> ### Aliases: bayescan
> ### Keywords: outlier hybridization genome scan
> 
> ### ** Examples
> 
> ## Not run
> hybrids<-hybridsim(Nmarker=100, Na=30, Nb=30, Nf1=30, type="selection", Nsel=25, hybrid="F1", S=100)
> outbayes<-bayescan(hybrids, filename="bayescanresults", nbp=10, pilot=50, burn=100)
sh: 1: bayescan_2.1: not found
[1] "Bayescan_2.1 not found"
> outbayes
NULL
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>