> Dear Robert,
>
> I get the following warning in the plotSNp function:
>
>  plotSnp(graph.par, chr.hmm)
> [1] "Adding 'grey40' as a color for missing genotype.  See getPar  
> for changing the defaults colors."
>
> Warning message:
> In .recycle(op$col, object) :
>   The length of the vector to be recycled is less than the number  
> of genotype calls
>
>

if

length(unique(genotype(yourHmmSnpSetObject)))

is greater than 3, then I assume that there is a missing genotype (a  
value that is not 1 (AA), 2 (AB), or 3 (BB)).  The plot should work  
fine, but it might be useful to know that there is a 4th value --  
hence the warning.

Rob






	[[alternative HTML version deleted]]

