[BioC] VariantAnnotation updated - error in predictCoding

[Valerie Obenchain]

The man page was a little out of date - which was probably a source of 
your confusion. Sorry about that.  An updated page is now in v 1.1.32.

Valerie

On 01/31/2012 08:15 AM, Valerie Obenchain wrote:
> 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 at ucl.ac.uk<mailto:f.lescai at ucl.ac.uk>
>> phone: +44.(0)207.905.2274
>> [ext: 2274]
>> --------------------------------------------------------------------------------
>>
>
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