[BioC] VariantAnnotation - MatrixToSnpMatrix - only returns NAs

[Lavinia Gordon]

Hi, I have just started working with VCF files and have discovered the VariantAnnotation package, many thanks for making these functions available.
Following the code outlined in the reference manual for MatrixToSnpMatrix, my VCF returns only NA values:
> head(geno(vcf)$GT)
           GHS008 GHS015 GHS025 GHS026 GHS027 GHS031 GHS033 GHS034 GHS036
chrM:73    "1/1"  "0/0"  "1/1"  "0/0"  "0/0"  "1/1"  "0/0"  "0/0"  "0/0" 
chrM:119   "0/0"  "0/0"  "0/0"  "1/1"  "1/1"  "0/0"  "0/0"  "0/0"  "0/0" 
rs72619361 "0/0"  "1/1"  "0/0"  "0/0"  "0/0"  "0/0"  "1/1"  "1/1"  "1/1" 
chrM:150   "1/1"  "1/1"  "1/1"  "1/1"  "1/1"  "1/1"  "1/1"  "1/1"  "1/1" 
chrM:189   "0/0"  "0/0"  "0/0"  "1/1"  "1/1"  "0/0"  "0/0"  "0/0"  "0/0" 
chrM:195   "1/1"  "1/1"  "1/1"  "0/0"  "0/0"  "1/1"  "1/1"  "1/1"  "1/1" 
> head(t(as(mat$genotype, "character")))
           GHS008 GHS015 GHS025 GHS026 GHS027 GHS031 GHS033 GHS034 GHS036
chrM:73    "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"  
chrM:119   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"  
rs72619361 "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"  
chrM:150   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"  
chrM:189   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"  
chrM:195   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"  

I have run the reference manual code with the supplied VCF and it all looks good.
I have no reason to suspect that there is anything wrong with my VCF.
Could anyone give me any tips as to how I can troubleshoot this and work out why all the NAs are appearing?

Many thanks,

Lavinia Gordon
Senior Research Officer
Quantitative Sciences Core, Bioinformatics

Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Road Parkville Victoria 3052 Australia 
T 03 8341 6221
www.mcri.edu.au

> vcf
class: VCF 
dim: 4665545 9 
genome: hg19 
exptData(1): header
fixed(4): REF ALT QUAL FILTER
info(19): AC AF ... SB EFF
geno(5): AD DP GQ GT PL
rownames(4665545): chrM:73 chrM:119 ... chrUn_gl000249:14244
  chrUn_gl000249:16222
rowData values names(1): paramRangeID
colnames(9): GHS008 GHS015 ... GHS034 GHS036
colData names(1): Samples

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] snpStats_1.8.1          Matrix_1.0-10           lattice_0.20-13        
 [4] survival_2.37-2         VariantAnnotation_1.4.6 Rsamtools_1.10.2       
 [7] Biostrings_2.26.2       GenomicRanges_1.10.6    IRanges_1.16.4         
[10] BiocGenerics_0.4.0      BiocInstaller_1.8.3    

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.20.3   Biobase_2.18.0         biomaRt_2.14.0        
 [4] bitops_1.0-5           BSgenome_1.26.1        DBI_0.2-5             
 [7] GenomicFeatures_1.10.1 grid_2.15.2            parallel_2.15.2       
[10] RCurl_1.95-3           RSQLite_0.11.2         rtracklayer_1.18.2    
[13] stats4_2.15.2          tools_2.15.2           XML_3.95-0.1          
[16] zlibbioc_1.4.0        

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