# Reading in FAMuSS data:
fms <- read.delim("http://people.umass.edu/foulkes/asg/data/FMS_data.txt", header=T, sep="\t")

# Necessary code from Example 3.9:
attach(fms)
NamesAkt1Snps <- names(fms)[substr(names(fms),1,4)=="akt1"]
FMSgeno <- fms[,is.element(names(fms),NamesAkt1Snps)]
FMSgenoNum <- data.matrix(FMSgeno)
FMSgenoNum[is.na(FMSgenoNum)] <- 4

# Exammple 3.11 (Principal components analysis (PCA) for identifying population substructure):
PCFMS <- prcomp(FMSgenoNum)
plot(PCFMS$"x"[,1],PCFMS$"x"[,2],xlab="PC1",ylab="PC2")