Question: motifbreakR VariantAnnotation namespace error on reading vcf file
0
gravatar for ashley.doane
4.0 years ago by
ashley.doane20
United States
ashley.doane20 wrote:

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")
ADD COMMENTlink modified 4.0 years ago by Simon Coetzee50 • written 4.0 years ago by ashley.doane20

There problem is in snps.from.file() function. I've contacted the author.

Valerie

ADD REPLYlink written 4.0 years ago by Valerie Obenchain6.7k
Answer: motifbreakR VariantAnnotation namespace error on reading vcf file
0
gravatar for Simon Coetzee
4.0 years ago by
USA Cedars-Sinai Medical Center
Simon Coetzee50 wrote:

Yes, there was a problem in the snps.from.file function. Thanks for the extra eyes. Fixed it up, it should be in the next build of the package, 1.0.1, tomorrow. Or you can get it from github now.

ADD COMMENTlink written 4.0 years ago by Simon Coetzee50
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