The man page was a little out of date - which was probably a source of your confusion.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] >> ------------------------------------------------------------------- ------------- >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor