I have some old code that's stopped working since I upgraded to R2.15 due to the unpackVcf method not being found. Is this still in the devel branch? or has it been deprecated completely? Or does anyone know another workaround I can use? thanks -s > vcfScan <- scanVcf(file_name) There were 50 or more warnings (use warnings() to see the first 50) > scanVcfHeader(file_name) class: VCFHeader samples(3): Fd03_high.vcf Fd03_low.vcf Fd03_zero.vcf meta(2): fileformat samtoolsVersion fixed(0): info(21): DP DP4 ... AC AN geno(7): DP4 GT ... SP PL > vcf <- unpackVcf(vcfScan, vcftab, info=TRUE, geno=TRUE) Error: could not find function "unpackVcf" > sessionInfo() R version 2.15.2 (2012-10-26) 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] splines stats4 grid stats graphics grDevices utils datasets methods base other attached packages: [1] VariantAnnotation_1.4.7 GGtools_4.6.2 GGBase_3.20.0 snpStats_1.8.1 Matrix_1.0-10 [6] survival_2.37-2 ShortRead_1.16.3 latticeExtra_0.6-24 RColorBrewer_1.0-5 Rsamtools_1.10.2 [11] lattice_0.20-13 Biostrings_2.26.3 gridExtra_0.9.1 zoo_1.7-9 plyr_1.8 [16] rtracklayer_1.18.2 GenomicRanges_1.10.6 IRanges_1.16.4 BiocGenerics_0.4.0 ggbio_1.6.6 [21] ggplot2_0.9.3 BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] AnnotationDbi_1.20.3 BSgenome_1.26.1 Biobase_2.18.0 DBI_0.2-5 GenomicFeatures_1.10.1 [6] Hmisc_3.10-1 MASS_7.3-23 RCurl_1.95-3 RSQLite_0.11.2 XML_3.95-0.1 [11] annotate_1.36.0 biomaRt_2.14.0 biovizBase_1.6.2 bit_1.1-9 bitops_1.0-4.2 [16] cluster_1.14.3 colorspace_1.2-1 dichromat_2.0-0 digest_0.6.1 ff_2.2-10 [21] genefilter_1.40.0 gtable_0.1.2 hwriter_1.3 labeling_0.1 munsell_0.4 [26] parallel_2.15.2 proto_0.3-10 reshape2_1.2.2 scales_0.2.3 stringr_0.6.2 [31] tools_2.15.2 xtable_1.7-0 zlibbioc_1.4.0 -- Seth Redmond Unité Génetique et Génomique des Insectes Vecteurs Institut Pasteur 28,rue du Dr Roux 75724 PARIS seth.redmond@pasteur.fr [[alternative HTML version deleted]]

Hi Seth, The .unpackVcf* functions are still there but they aren't (never have been) exported. You need to use ::: to get at them. VariantAnnotation:::.unpackVcf readVcf() is much more direct if a VCF object is your end goal. Valerie On 01/29/2013 08:04 AM, seth redmond wrote: > I have some old code that's stopped working since I upgraded to R2.15 due to the unpackVcf method not being found. Is this still in the devel branch? or has it been deprecated completely? > > Or does anyone know another workaround I can use? > > thanks > > -s > > > > >> vcfScan<- scanVcf(file_name) > There were 50 or more warnings (use warnings() to see the first 50) >> scanVcfHeader(file_name) > class: VCFHeader > samples(3): Fd03_high.vcf Fd03_low.vcf Fd03_zero.vcf > meta(2): fileformat samtoolsVersion > fixed(0): > info(21): DP DP4 ... AC AN > geno(7): DP4 GT ... SP PL >> vcf<- unpackVcf(vcfScan, vcftab, info=TRUE, geno=TRUE) > Error: could not find function "unpackVcf" >> sessionInfo() > R version 2.15.2 (2012-10-26) > 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] splines stats4 grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] VariantAnnotation_1.4.7 GGtools_4.6.2 GGBase_3.20.0 snpStats_1.8.1 Matrix_1.0-10 > [6] survival_2.37-2 ShortRead_1.16.3 latticeExtra_0.6-24 RColorBrewer_1.0-5 Rsamtools_1.10.2 > [11] lattice_0.20-13 Biostrings_2.26.3 gridExtra_0.9.1 zoo_1.7-9 plyr_1.8 > [16] rtracklayer_1.18.2 GenomicRanges_1.10.6 IRanges_1.16.4 BiocGenerics_0.4.0 ggbio_1.6.6 > [21] ggplot2_0.9.3 BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.20.3 BSgenome_1.26.1 Biobase_2.18.0 DBI_0.2-5 GenomicFeatures_1.10.1 > [6] Hmisc_3.10-1 MASS_7.3-23 RCurl_1.95-3 RSQLite_0.11.2 XML_3.95-0.1 > [11] annotate_1.36.0 biomaRt_2.14.0 biovizBase_1.6.2 bit_1.1-9 bitops_1.0-4.2 > [16] cluster_1.14.3 colorspace_1.2-1 dichromat_2.0-0 digest_0.6.1 ff_2.2-10 > [21] genefilter_1.40.0 gtable_0.1.2 hwriter_1.3 labeling_0.1 munsell_0.4 > [26] parallel_2.15.2 proto_0.3-10 reshape2_1.2.2 scales_0.2.3 stringr_0.6.2 > [31] tools_2.15.2 xtable_1.7-0 zlibbioc_1.4.0 > > > -- > Seth Redmond > Unit? G?netique et G?nomique des Insectes Vecteurs > Institut Pasteur > 28,rue du Dr Roux > 75724 PARIS > seth.redmond at pasteur.fr > > > [[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