I been using GGtools but have a couple of questions .

 First about  the snpMeta class that can be generated using the
thinHM2meta or df2snpMeta. Both of these documented commands show cases
where one chromosome is done at a time. How does one handle the case for
more than one chromosome,  that is using snpScreen with dome over more
than one chromosome?  The snpMeta class has both meta and chromosome
slots but its not clear (to me) how to load data from more than one
chromosome, or if that can/should be done.

Second I have snpScreen   failing when I use a gene "ARTS-1" - see below
. I wonder if it's something trivial (ARTS-1 not in the hgfocus arrys
used in this example?) but can see what is going on in snpScreen as
"snpScreen" in R does not return much info about the function:

> snpScreen
standardGeneric for "snpScreen" defined from package "GGtools"

function (racExSet, snpMeta, gene, formTemplate, fitter, gran, 
    ...) 
standardGeneric("snpScreen")
<environment: 0x027c2d78>
Methods may be defined for arguments: racExSet, snpMeta, gene,
formTemplate, fitter, gran 


 
The error:


> a.screen<-snpScreen(chr20GGdem, chr20meta, genesym("CPNE1"), ~.,
fastAGMfitter)
Warning message:
In .local(racExSet, snpMeta, gene, formTemplate, fitter, gran, ...) :
  some genotype results had missing values; associated SNPs are dropped
completely in this version when fastAGM is used.
> a.screen<-snpScreen(chr20GGdem, chr20meta, genesym("ARTS-1"), ~.,
fastAGMfitter)
Error in .local(racExSet, snpMeta, gene, formTemplate, fitter, gran,
...) : 
  subscript out of bounds
> sessionInfo()
R version 2.6.1 (2007-11-26) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods

[8] base     

other attached packages:
 [1] GGtools_1.6.1       mgu74av2_2.0.1      geneplotter_1.16.0 
 [4] lattice_0.17-2      annotate_1.16.1     xtable_1.5-2       
 [7] AnnotationDbi_1.0.6 RSQLite_0.6-4       DBI_0.2-4          
[10] hgfocus_2.0.1       Biobase_1.16.2     

loaded via a namespace (and not attached):
[1] grid_2.6.1         KernSmooth_2.22-21 RColorBrewer_1.0-2
> 
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