[BioC] gwSnpTests in GGtools

[francy [guest]]

Hi all,

I am trying to find eQTLs in or around a particular gene with probe ID= "10023813203" (gene is APOE). I have first selected the SNPs on only my chromosome of interest (chr19), then imported the plink files only for this chromosome doing this:
    
    snp.matrix<-read.plink("plink.bed", "plink.bim", "plink.fam",select.snps=chr19)

I was able to create an expression set (called 'es'), and a sml_Set by doing this:

    ss<- make_smlSet(es, list("1"=snp.matrix$genotypes)) 

but I can't seem to go beyond and use this sml_Set to perform the association. 

When I try this or other combinations of this (e.g. using 'APOE')
    f1 = gwSnpTests(probeId("10023813203"), ss)

Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "gwSnpTests", for signature "character", "smlSet", "missing", "missing"

My first question is, why is the 'gwSnpTests' not working? 
My second question is, do I have to select the chromosome I am interested in before creating the sml test? I would have liked to select chromosome 19 after so that I could analyse more than this one chromosome if I wanted to…Is this possible?? It seems as the snp.matrix must be in the form of a list, so maybe I have to create a list of all the chromosomes?
THANK YOU VERY VERY MUCH FOR ANY HELP YOU COULD GIVE ME!! I really appreciate it!

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] GGtools_3.10.2       ff_2.2-3             bit_1.1-7           
 [4] GenomicRanges_1.4.8  org.Hs.eg.db_2.5.0   rtracklayer_1.12.5  
 [7] RCurl_1.6-10         bitops_1.0-4.1       IRanges_1.10.6      
[10] annotate_1.30.1      AnnotationDbi_1.14.1 GGBase_3.12.0       
[13] RSQLite_0.10.0       DBI_0.2-5            snpStats_1.2.1      
[16] Matrix_0.999375-50   lattice_0.19-33      survival_2.36-9     
[19] Biobase_2.12.2      

loaded via a namespace (and not attached):
[1] Biostrings_2.20.4 BSgenome_1.20.1   grid_2.13.1       XML_3.4-3        
[5] xtable_1.5-6     


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