Much more straightforward, the workflow is much simpler this way. thanks very much, it works great. Francesco On 31 Jan 2012, at 16:28, Valerie Obenchain wrote: The man page was a little out of date - which was probably a source of your confusion.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@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@u cl.ac.uk=""> phone: +44.(0)207.905.2274 [ext: 2274] ---------------------------------------------------------------------- ---------- [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ---------------------------------------------------------------------- ----------- 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] ---------------------------------------------------------------------- ---------- [[alternative HTML version deleted]]