Question: unpackVcf not found
0
gravatar for seth redmond
6.9 years ago by
seth redmond70
seth redmond70 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 Unité Génetique et Génomique des Insectes Vecteurs Institut Pasteur 28,rue du Dr Roux 75724 PARIS seth.redmond@pasteur.fr [[alternative HTML version deleted]]
• 424 views
ADD COMMENTlink modified 6.9 years ago by Valerie Obenchain6.7k • written 6.9 years ago by seth redmond70
Answer: unpackVcf not found
0
gravatar for Valerie Obenchain
6.9 years ago by
United States
Valerie Obenchain6.7k wrote:
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
ADD COMMENTlink written 6.9 years ago by Valerie Obenchain6.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 290 users visited in the last hour