indpca: PCA on a matrix of individuals genotypes frequencies

In hierfstat: Estimation and Tests of Hierarchical F-Statistics

PCA on a matrix of individuals genotypes frequencies

Description

Carry out a PCA on the centered, unscaled matrix of individual's allele frequencies.

Usage

indpca(dat,ind.labels=NULL,scale=FALSE)

## S3 method for class 'indpca'
print(x,...)
## S3 method for class 'indpca'
plot(x,eigen=FALSE,ax1=1,ax2=2,...)

Arguments

dat	A data frame with population of origin as first column, and genotypes in following columns.
ind.labels	a vector of labels for the different individuals
scale	whether to standardize each column to variance 1 or to leave it as is (default)
x	an indpca object
eigen	whether to plot in an additional windows screeplot of the inertias for the different axes
ax1	which PCA coordinates to plot on the x axis
ax2	which PCA coordinates to plot on the y axis
...	further arguments to pass to print or plot

Value

An object of class indpca with components

call	The function call
ipca	an object of class pca and dudi (see dudi.pca) in package ade4
mati	the original non centered matrice of individuals X alleles frequencies

Author(s)

Jerome Goudet [e-mail]

Examples

##not run
data(gtrunchier)
x<-indpca(gtrunchier[,-2],ind.labels=gtrunchier[,2])
plot(x,col=gtrunchier[,1],cex=0.7)

hierfstat documentation built on May 6, 2022, 1:05 a.m.