PopGenome (version 2.1.6)

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

# 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