I have been merrily using the genetics package and more specifically have
been using the makeGenotypes and genotypes function. I check my
accomplishments by going
> class(g2)
[1] "genotype" "factor"
and likewise
> class(g1)
[1] "genotype" "factor"
Yet when I execute a command such as allele count I get this
> allele.count(g1)
D I
[1,] 2 0
[2,] 1 1
[3,] 2 0
[4,] 0 2
[5,] 2 0
[6,] 2 0
[7,] 2 0
[8,] 2 0
[9,] 0 2
[10,] NA NA
> allele.count(g2)
list()
If I print the objects I get this
> g1
[1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" NA
Alleles: D I
> g2
[1] "1/1" "1/1" "1/1" "1/1" "1/1" "1/1" "1/1" "1/1" "2/2" "1/1" "2/2" "1/1"
"1/1" "1/1"
Alleles:
Clearly g1 and g2 are not exactly the same even though they are the same
class.
I can make g2 behave as g1 if i type
g3<-genotype(g2)
g3 then behaves as it should.
The issue may have arrisen since g2 is just a subset of a much bigger object
that was created using reshape command in the base package or maybe melt and
cast in the reshape package. Can anyone enlighten me?
--
Farrel Buchinsky
Mobile: (412) 779-1073
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