bayescan: Identifying candidate loci under natural selection with...
In fbalao/AFLPsim: Hybrid Simulation and Genome Scan for Dominant Markers

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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

`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).

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.

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

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

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.

gscan sim2bayescan

## 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