Hi Francesco,

I changed the requirements of the varAllele argument from character to 
either DNAStringSet or missing. Allowing the varAllele to be a character 
name of a metadatacolumn was problematic.

 > showMethods("predictCoding")
Function: predictCoding (package VariantAnnotation)
query="GRanges", subject="TranscriptDb", seqSource="ANY", 
varAllele="DNAStringSet"
query="Ranges", subject="TranscriptDb", seqSource="ANY", 
varAllele="DNAStringSet"
query="VCF", subject="TranscriptDb", seqSource="ANY", varAllele="missing"

I've also added a method for the query to be a VCF object so you can 
just pass the VCF which allows you bypass the "flattening" step. When 
you pass a VCF as the query the varAllele argument will be missing; it 
is taken from the VCF internally with values(alt(<VCF>))[["ALT"]]. An 
example of this usage is on the man page. The output of this function 
now includes all of txID, geneID and cdsID.

Valerie


On 01/31/2012 06:00 AM, Lescai, Francesco wrote:
> Hi there,
> I just updated my packages and I have now an error from predictCoding 
> in VariantAnnotation_1.1.31 I didn't have with VariantAnnotation_1.1.30.
>
> Here's my code.
> Thanks,
> Francesco
>
>
> > consequences.snps <- predictCoding(
> +                 query=flat.snps,
> +                 subject=txdb19,
> +                 seqSource=Hsapiens,
> +                 varAllele="ALT")
> *Error in function (classes, fdef, mtable)  : *
> *  unable to find an inherited method for function "predictCoding", 
> for signature "GRanges", "TranscriptDb", "BSgenome", "character"*
>
> /> sessionInfo()/
> /R Under development (unstable) (2012-01-20 r58146)/
> /Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)/
> /
> /
> /locale:/
> /[1] C/en_US.UTF-8/C/C/C/C/
> /
> /
> /attached base packages:/
> /[1] stats     graphics  grDevices utils     datasets  methods   base /
> /
> /
> /other attached packages:/
> / [1] BSgenome.Hsapiens.UCSC.hg19_1.3.17      BSgenome_1.23.2         
>                 TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 
> GenomicFeatures_1.7.10 /
> / [5] VariantAnnotation_1.1.31                Rsamtools_1.7.23         
>                Biostrings_2.23.6                       
> AnnotationDbi_1.17.11 /
> / [9] Biobase_2.15.3                          GenomicRanges_1.7.16     
>                IRanges_1.13.20                         
> BiocGenerics_0.1.4 /
> /[13] BiocInstaller_1.3.7 /
> /
> /
> /loaded via a namespace (and not attached):/
> / [1] DBI_0.2-5          Matrix_1.0-3       RCurl_1.9-5       
>  RSQLite_0.11.1     XML_3.8-0          biomaRt_2.11.1     
> bitops_1.0-4.1     grid_2.15.0 /
> / [9] lattice_0.20-0     rtracklayer_1.15.6 snpStats_1.5.2     
> splines_2.15.0     survival_2.36-10   tools_2.15.0       zlibbioc_1.1.1 /
>
>
> ---------------------------------------------------------------------------------
> *Francesco Lescai, PhD, EDBT*
> Senior Research Associate in Genome Analysis
> University College London
> Faculty of Population Health Sciences
> Dept. Genes, Development & Disease
> ICH - Molecular Medicine Unit, GOSgene team
> 30 Guilford Street
> WC1N 1EH London UK
>
> email: f.lescai@ucl.ac.uk <mailto:f.lescai@ucl.ac.uk>
> phone: +44.(0)207.905.2274
> [ext: 2274]
> --------------------------------------------------------------------------------
>


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