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

In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

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"

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The following Slots will be filled
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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

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.