R help - Dec 2006 - Genotypes are not all the same

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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Farrel Buchinsky <fjbuch <at> gmail.com>
writes:
> 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?
genotype class behaves internally much like factor class. I guess that
levels/alleles were dropped somewhere. You have to figure out where this 
happened.

Gregor