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h.draisma
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@hdraisma-15174
Last seen 7.7 years ago
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
