PopGenome (version 2.7.5)

BayeScanR: An R implementation of BayeScan (Foll \& Gagiotti 2008)

Description

BayeScanR is an R implementation of BayeScan for analysis of codominant markers.

Usage

BayeScanR(input,nb.pilot=10,pilot.runtime=2500,main.runtime=100000, discard=50000)

Arguments

input

textfile or an R-object returned by getBayes()

nb.pilot

number of pilot runs

pilot.runtime

length of pilot runs

main.runtime

length of main runs

discard

how many runs in the main.loop should be discarded?

Value

returned value is an object of class "BAYESRETURN" -------------------------------------------------------------- The following Slots will be filled --------------------------------------------------------------

alpha

alpha effects

beta

beta effects

var_alpha

variance of alpha values

a_inc

which alpha is included in the model

fst

FST values

P

P-value

References

[1] Foll M and OE 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 {
# GENOME.class <- readData("...\Alignments")
# GENOME.class <- F_ST.stats(GENOME.class,list(1:5,6:10))
# Bayes.input  <- getBayes(GENOME.class)
# BAYES.class  <- BayeScanR(Bayes.input)
# BAYES.class

# }