Factors are a new vector comprised of integer values with a corresponding
character value. They are categorical variables.
A good way to describe this is when thinking of an Olympic roster.
There’s hundreds of athlete names, and under “medal type” there would be a
factor with four levels: gold, silver, bronze, and none.
R can assign numbers to these factors when doing analysis
(so, in the case of alleles, AA=3, Aa=2, aa=1 could be an assignment).
To store a vector as a variable of a factor,
use variable <- factor(vectorname).
Their integer assignments can be checked with as.integer(variable),
and the levels can be checked with levels(variable).
> allele <- c( 'aa', 'Aa', 'AA', 'aa', 'aa', 'aa', 'aa', 'Aa', 'Aa')
> types <- factor(allele)
> print(types)
[1] aa Aa AA aa aa aa aa Aa Aa
Levels: aa Aa AA
> as.integer(types)
[1] 1 2 3 1 1 1 1 2 2
> levels(types)
[1] "aa" "Aa" "AA"