run_G: run_G

In jrobledob/SSBayesCH: What the Package Does (One Line, Title Case)

Description

Performs the two-step approach for detecting selection signatures using genomic data from diploid individuals and biallelic markers developed by Gianola et al. (2010).

Usage

run_G(Data,N.Groups,Prior,N.Samples,Pop.col,Geno.cols,Sel.SNP='TRUE',
tailp=0.05,Prior.neutral)

Arguments

Data	A data frame or matrix containing genotypic data from m markers as well as a column indicating the subpopulation to which the individual belongs. Subpopulations must be coded using consecutive integer numbers starting from 1.
N.Groups	A vector containing integers corresponding to the number of groups to be fitted in the finite mixture model.
Prior	A vector of dimension 2 containing the values of model the 'full model' hyperparameters (positive real numbers).
N.Samples	Integer corresponding to the number of samples used to perform the Monte Carlo estimation of the Fst parameter.
Pop.col	Integer indicating the column that contains the subpopulation each individual belongs to.
Geno.cols	Vector containing the columns corresponding to genotypes in the input dataset.
Sel.SNP	Logical. If TRUE, markers are selected using the rule defined by Gianola et al. (2010), if FALSE all markers are set as 'selected' and consequently all their estimated Fst values are used in the clustering step. The default value es TRUE.
tailp	Numeric value indicating the tail probability used to declare a value as extreme under the null posterior distribution of Fst. The default value is 0.05
Prior.neutral	A vector of dimension 2 containing the values of model hyperpameters (positive real numbers) for the 'null model'.

Value

A list containing the following objects. N_Groups. The selected number of groups used to cluster markers. Groups. The group memberships. Group.sizes. The number of markers in each group. Post.means The estimated posterior means of Fst under the 'full model'. NCandidateLoci. The number of selected loci. Selected_Loci. The ID's of the selected loci.

Author(s)

Carlos Alberto Martínez Niño ([e-mail]).

References

Gianola, D., Simianer, H., Qanbari, S. 2010. A two-step method for detecting selection signatures using genetic markers. Genetic Research Cambridge, 92; 141-155.

jrobledob/SSBayesCH documentation built on Dec. 21, 2021, 3:15 a.m.