COR_Fstd: Function for calculating pairwise Fst and correlation...

In xinghuq/HierDpart: Partitioning Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems

Function for calculating pairwise Fst and correlation coefficient between Fst (Weir and Cockerham, 1984) and geographic distance

Description

This function calculates pairwise genetic differentiation (Fst), as well as the correlation coefficient between genetic differentiation (Fst) and geographic distance.

Usage

COR_Fstd(x, d, ncode,nrepet)

Arguments

x	A genetic data files, here the format is genepop format.
d	Pairwise geographic distance for calculating correlations. If no actual geographic distance, d=NULL. The geographic distance should be a matrix that corresponds to the pairwise genetic differentiation matrix.
ncode	The code type of the genotype.
nrepet	Number of permutations.

Details

This function returns lists of pairwise Fst matrix, and a matrix of theorical geographical distance if d is NULL, as well as the correlation coefficient.

Value

pwFst	The pairwise genetic differentiation (Fst) matrix.
COR_Fstd	Pearson correlation coefficient between genetic differentiation (Fst) and geographic distance.

Author(s)

[e-mail]

References

Qin, X., & Gaggiotti, O. E. (2022). Information-based summary statistics for spatial genetic structure inference. Molecular Ecology Resources, 22(6), 2183-2195.

Goudet, J. (2005). Hierfstat, a package for R to compute and test hierarchical F-statistics. Molecular Ecology Notes, 5(1), 184-186.

Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24 (11), 1403-1405.

Weir, B.S. (1996) Genetic Data Analysis II. Sinauer Associates.

Weir B.S. and Cockerham C.C. (1984) Estimating F-Statistics for the Analysis of Population Structure. Evolution 38:1358

Evolution and the Genetics of Populations Volume 2: the Theory of Gene Frequencies, pg 294-295, S. Wright, Univ. of Chicago Press, Chicago, 1969.

See Also

COR_detaDd

Examples

# example genepop file, the example file is a complicated hierarchical island model
f1 <- function(f) system.file("extdata", f,package="HierDpart")
#d2=COR_Fstd(f1("Island.gen"),d=NULL,ncode=3,nrepet=999)
#print(d2)

xinghuq/HierDpart documentation built on March 21, 2023, 6:43 p.m.