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Hi I'm encountered the following error while reading a vcf file using the motifbreakR package.
vcf <- "/Users/asd2007/Tools/vcftools/examples/annotate-test.vcf" vars <- snps.from.file(file =vcf, search.genome = BSgenome.Hsapiens.UCSC.hg19, format = "vcf")
Error: 'seqlevels<-' is not an exported object from 'namespace:VariantAnnotation'
I am able to read this vcf using succesfully with the following line:
readVcf(vcf, "hg19")
However, it is not immediately obvious to me whether motifbreakR would accept this format.
> sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.1 (El Capitan) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] VariantAnnotation_1.16.1 Rsamtools_1.22.0 SummarizedExperiment_1.0.0 Biobase_2.30.0 BSgenome.Hsapiens.UCSC.hg19_1.4.0 [6] motifbreakR_1.0.0 MotifDb_1.12.0 BSgenome_1.38.0 rtracklayer_1.30.1 Biostrings_2.38.0 [11] XVector_0.10.0 GenomicRanges_1.22.0 GenomeInfoDb_1.6.0 IRanges_2.4.1 S4Vectors_0.8.0 [16] BiocGenerics_0.16.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.1 locfit_1.5-9.1 biovizBase_1.18.0 lattice_0.20-33 digest_0.6.8 plyr_1.8.3 futile.options_1.0.0 [8] acepack_1.3-3.3 RSQLite_1.0.0 ggplot2_1.0.1.9003 MotIV_1.26.0 zlibbioc_1.16.0 GenomicFeatures_1.22.0 annotate_1.48.0 [15] rpart_4.1-10 proto_0.3-10 splines_3.2.2 BiocParallel_1.4.0 stringr_1.0.0 geneplotter_1.48.0 foreign_0.8-66 [22] RCurl_1.95-4.7 biomaRt_2.26.0 munsell_0.4.2 compiler_3.2.2 seqLogo_1.36.0 Gviz_1.14.0 nnet_7.3-11 [29] gridExtra_2.0.0 Hmisc_3.17-0 matrixStats_0.15.0 XML_3.98-1.3 TFMPvalue_0.0.5 GenomicAlignments_1.6.1 bitops_1.0-6 [36] xtable_1.7-4 gtable_0.1.2 DBI_0.3.1 magrittr_1.5 scales_0.3.0 stringi_1.0-1 genefilter_1.52.0 [43] RcppArmadillo_0.6.100.0.0 ggthemes_2.2.1 latticeExtra_0.6-26 futile.logger_1.4.1 grImport_0.9-0 Formula_1.2-1 rGADEM_2.18.0 [50] lambda.r_1.1.7 RColorBrewer_1.1-2 tools_3.2.2 dichromat_2.0-0 ade4_1.7-2 DESeq2_1.10.0 survival_2.38-3 [57] AnnotationDbi_1.32.0 colorspace_1.2-6 cluster_2.0.3 motifStack_1.14.0 > BiocInstaller::biocValid() * sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.1 (El Capitan) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] VariantAnnotation_1.16.1 Rsamtools_1.22.0 SummarizedExperiment_1.0.0 Biobase_2.30.0 BSgenome.Hsapiens.UCSC.hg19_1.4.0 [6] motifbreakR_1.0.0 MotifDb_1.12.0 BSgenome_1.38.0 rtracklayer_1.30.1 Biostrings_2.38.0 [11] XVector_0.10.0 GenomicRanges_1.22.0 GenomeInfoDb_1.6.0 IRanges_2.4.1 S4Vectors_0.8.0 [16] BiocGenerics_0.16.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.1 locfit_1.5-9.1 biovizBase_1.18.0 lattice_0.20-33 digest_0.6.8 plyr_1.8.3 futile.options_1.0.0 [8] acepack_1.3-3.3 RSQLite_1.0.0 BiocInstaller_1.20.0 ggplot2_1.0.1.9003 MotIV_1.26.0 zlibbioc_1.16.0 GenomicFeatures_1.22.0 [15] annotate_1.48.0 rpart_4.1-10 proto_0.3-10 splines_3.2.2 BiocParallel_1.4.0 stringr_1.0.0 geneplotter_1.48.0 [22] foreign_0.8-66 RCurl_1.95-4.7 biomaRt_2.26.0 munsell_0.4.2 compiler_3.2.2 seqLogo_1.36.0 Gviz_1.14.0 [29] nnet_7.3-11 gridExtra_2.0.0 Hmisc_3.17-0 matrixStats_0.15.0 XML_3.98-1.3 TFMPvalue_0.0.5 GenomicAlignments_1.6.1 [36] bitops_1.0-6 xtable_1.7-4 gtable_0.1.2 DBI_0.3.1 magrittr_1.5 scales_0.3.0 stringi_1.0-1 [43] genefilter_1.52.0 RcppArmadillo_0.6.100.0.0 ggthemes_2.2.1 latticeExtra_0.6-26 futile.logger_1.4.1 grImport_0.9-0 Formula_1.2-1 [50] rGADEM_2.18.0 lambda.r_1.1.7 RColorBrewer_1.1-2 tools_3.2.2 dichromat_2.0-0 ade4_1.7-2 DESeq2_1.10.0 [57] survival_2.38-3 AnnotationDbi_1.32.0 colorspace_1.2-6 cluster_2.0.3 motifStack_1.14.0 * Packages too new for Bioconductor version '3.2' Version LibPath ggplot2 "1.0.1.9003" "/Library/Frameworks/R.framework/Versions/3.2/Resources/library" downgrade with biocLite("ggplot2")
There problem is in snps.from.file() function. I've contacted the author.
Valerie