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Question: "> example(coMET)" returns error in snpBiomart() call
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gravatar for h.draisma
9 months ago by
h.draisma0
h.draisma0 wrote:

Dear Tiphaine,

Thank you for your response. No worries.

I was wondering which manual you are referring to? In the Vignette for the current version of 'coMET' (1.10.2) I can't find such a reference that the name of the genes*ENSEMBL() function to be used has changed.

Also, I tried to run the examples from the "Examples" section on the coMET::comet() help page in <R> using a call to genes_ENSEMBL() instead of a call to genesENSEMBL(), as you indicate -- this gave me a different (new) error:

 

Error in snpBiomart(chrom, start, end, dataset = "hsapiens_snp_som", showId = FALSE) :
  could not find function "snpBiomart"


Please find below the code that I tried to execute in <R>, and the result -- please note that in the code from the coMET::comet() help page "Examples" section I only replaced "genesENSEMBL" by "genes_ENSEMBL" indeed, as you indicated:

> require(coMET)
> extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
> configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt")
> myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
> myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
> mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
>
> chrom <- "chr2"
> start <- 38290160
> end <- 38303219
> gen <- "hg38"
>
> if(interactive()){
+   cat("interactive")
+   genetrack <-genes_ENSEMBL(gen,chrom,start,end,showId=TRUE)
+   snptrack <- snpBiomart(chrom, start, end,
+                          dataset="hsapiens_snp_som",showId=FALSE)
+   strutrack <- structureBiomart(chrom, start, end,
+                                 strand, dataset="hsapiens_structvar_som")
+   clinVariant<-ClinVarMainTrack(gen,chrom,start,end)
+   clinCNV<-ClinVarCnvTrack(gen,chrom,start,end)
+   gwastrack <-GWASTrack(gen,chrom,start,end)
+   geneRtrack <-GeneReviewsTrack(gen,chrom,start,end)
+   listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
+                    clinCNV,gwastrack,geneRtrack)
+   comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file",
+         cormatrix.file=mycorrelation, cormatrix.type="listfile",
+         mydata.large.file=myexpressfile, mydata.large.type="listfile",
+         tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE,disp.pvalueplot=FALSE)
+ } else {
+   cat("Non interactive")
+   data(geneENSEMBLtrack)
+   data(snpBiomarttrack)
+   data(ISCAtrack)
+   data(strucBiomarttrack)
+   data(ClinVarCnvTrack)
+   data(clinVarMaintrack)
+   data(GWASTrack)
+   data(GeneReviewTrack)
+   listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
+                    clinCNV,gwastrack,geneRtrack)
+   comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file",
+         cormatrix.file=mycorrelation, cormatrix.type="listfile",
+         mydata.large.file=myexpressfile,  mydata.large.type="listfile",
+         tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE,disp.pvalueplot=FALSE)
+ }
interactive
Error in snpBiomart(chrom, start, end, dataset = "hsapiens_snp_som", showId = FALSE) :
  could not find function "snpBiomart"
> traceback()
No traceback available
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8   
 [6] LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] parallel  stats4    grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] coMET_1.10.2         trackViewer_1.14.1   ggbio_1.26.0         ggplot2_2.2.1        psych_1.7.8          Gviz_1.22.3          GenomicRanges_1.30.3
 [8] GenomeInfoDb_1.14.0  IRanges_2.12.0       S4Vectors_0.16.0     BiocGenerics_0.24.0  biomaRt_2.34.2      

loaded via a namespace (and not attached):
 [1] nlme_3.1-131                  ProtGenerics_1.10.0           bitops_1.0-6                  matrixStats_0.53.1            bit64_0.9-7                  
 [6] RColorBrewer_1.1-2            progress_1.1.2                httr_1.3.1                    tools_3.4.3                   backports_1.1.2              
[11] R6_2.2.2                      rpart_4.1-13                  Hmisc_4.1-1                   DBI_0.8                       lazyeval_0.2.1               
[16] colorspace_1.3-2              nnet_7.3-12                   gridExtra_2.3                 prettyunits_1.0.2             GGally_1.3.2                 
[21] mnormt_1.5-5                  RMySQL_0.10.14                bit_1.1-12                    curl_3.1                      compiler_3.4.3               
[26] graph_1.56.0                  Biobase_2.38.0                htmlTable_1.11.2              grImport_0.9-0                DelayedArray_0.4.1           
[31] rtracklayer_1.38.3            scales_0.5.0                  checkmate_1.8.5               pbapply_1.3-4                 RBGL_1.54.0                  
[36] stringr_1.3.0                 digest_0.6.15                 Rsamtools_1.30.0              foreign_0.8-69                XVector_0.18.0               
[41] base64enc_0.1-3               dichromat_2.0-0               htmltools_0.3.6               ensembldb_2.2.2               BSgenome_1.46.0              
[46] htmlwidgets_1.0               rlang_0.2.0                   rstudioapi_0.7                RSQLite_2.0                   BiocInstaller_1.28.0         
[51] shiny_1.0.5                   BiocParallel_1.12.0           acepack_1.4.1                 VariantAnnotation_1.24.5      RCurl_1.95-4.10              
[56] magrittr_1.5                  GenomeInfoDbData_1.0.0        Formula_1.2-2                 Matrix_1.2-11                 Rcpp_0.12.15                 
[61] munsell_0.4.3                 stringi_1.1.6                 yaml_2.1.17                   SummarizedExperiment_1.8.1    zlibbioc_1.24.0              
[66] plyr_1.8.4                    AnnotationHub_2.10.1          blob_1.1.0                    lattice_0.20-35               Biostrings_2.46.0            
[71] splines_3.4.3                 hash_2.2.6                    GenomicFeatures_1.30.3        knitr_1.20                    pillar_1.2.1                 
[76] reshape2_1.4.3                XML_3.98-1.10                 biovizBase_1.26.0             latticeExtra_0.6-28           data.table_1.10.4-3          
[81] httpuv_1.3.6.2                gtable_0.2.0                  reshape_0.8.7                 assertthat_0.2.0              mime_0.5                     
[86] xtable_1.8-2                  AnnotationFilter_1.2.0        colortools_0.1.5              survival_2.41-3               OrganismDbi_1.20.0           
[91] tibble_1.4.2                  GenomicAlignments_1.14.1      AnnotationDbi_1.40.0          memoise_1.1.0                 corrplot_0.84                
[96] cluster_2.0.6                 interactiveDisplayBase_1.16.0
>

 

Thank you,

Best regards

Harmen

ADD COMMENTlink modified 9 months ago • written 9 months ago by h.draisma0
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