GstH: Hedrick's G'st

In FinePop: Fine-Scale Population Analysis

Description

This function estimates pairwise G'st (Hedrick 2005) among subpopulations from a GENEPOP data object (Rousset 2008). Missing genotype values in the GENEPOP file ("0000" or "000000") are simply ignored.

Usage

GstH(popdata)

Arguments

popdata

Population data object created by read.genepop function from a GENEPOP file.

Value

Matrix of estimated pairwise Hedrick's G'st.

Author(s)

Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada

References

Hedrick P (2005) A standardized genetic differentiation measure. Evolution, 59, 1633-1638.

Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resources, 8, 103-106.

See Also

read.genepop

Examples

# Example of GENEPOP file
data(jsmackerel)
cat(jsmackerel$MS.genepop, file="JSM_MS_genepop.txt", sep="\n")
cat(jsmackerel$popname, file="JSM_popname.txt", sep=" ")

# Data load
# Prepare your GENEPOP file and population name file in the working directory
# (Here, these files were provided as "JSM_MS_genepop.txt" and "JSM_popname.txt".)
popdata <- read.genepop(genepop="JSM_MS_genepop.txt", popname="JSM_popname.txt")

# Hedrick's G'st estimation
result.GstH <- GstH(popdata)
write.csv(result.GstH, "result_GstH.csv", na="")
print(as.dist(result.GstH))

Example output

Calculating population 1:2 1:3 1:4 1:5 1:6 1:7 1:8 2:3 2:4 2:5 2:6 2:7 2:8 3:4 3:5 3:6 3:7 3:8 4:5 4:6 4:7 4:8 5:6 5:7 5:8 6:7 6:8 7:8  done.
               OS           HM2            BS           HI1           HI2
HM2  2.218787e-03                                                        
BS   2.692453e-03  7.108098e-03                                          
HI1 -5.415995e-03  4.453109e-03  6.382283e-03                            
HI2  1.859378e-05  1.332207e-03 -3.747562e-04  1.239922e-03              
HAa  7.817858e-02  6.090541e-02  7.277691e-02  8.260973e-02  6.920994e-02
HAb  2.257660e-01  2.586918e-01  2.223576e-01  2.374775e-01  2.601140e-01
HAr  3.943747e-02  2.289396e-02  2.857399e-02  3.740620e-02  2.811231e-02
              HAa           HAb
HM2                            
BS                             
HI1                            
HI2                            
HAa                            
HAb  2.876444e-01              
HAr  6.334892e-02  2.333396e-01

FinePop documentation built on May 2, 2019, 3:30 p.m.