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leekgroup / regionReport

Generate HTML report for a set of genomic regions or DESeq2/edgeR results
http://leekgroup.github.io/regionReport
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Error in mergeNamedAtomicVectors #11

Closed cboschi closed 2 years ago

cboschi commented 2 years ago

I am using regionReport to create a report from my defined regions in the cattle genome (no annotation provided):

report <- renderReport(regions, "Example bumphunter", pvalueVars = NULL, 
    densityVars = c("Area" = "area", "Value" = "value", "Cluster Length" = "clusterL"
    ), significantVar = NULL, output = "report", outdir = "report", device = "png")

I got an error in the annotation part regarding sequence lengths. I checked my regions, and there are regions with 1 base, so I am assuming this can be the issue.

No annotationPackage supplied. Trying org.Hs.eg.db.
Getting TSS and TSE.
Getting CSS and CSE.
Getting exons.
Annotating genes.
Quitting from lines 187-196 (DMR_report.Rmd) 
Error in mergeNamedAtomicVectors(seqlengths(x), seqlengths(y), what = c("sequence",  : 
  sequences chr8, chr2, chr3, chr18, chr19, chr11, chr10, chr17, chr14, chr4, chrX, chr9, chr21, chr1, chr13, chr5, chr6, chr16, chr7, chr12, chr15, chr20, chr22 have incompatible seqlengths:
  - in 'x': 113319770, 136231102, 121005158, 65820629, 63449741, 106982474, 103308737, 73167244, 82403003, 120000601, 139009144, 105454467, 69862954, 158534110, 83472345, 120089316, 117806340, 81013979, 110682743, 87216183, 85007780, 71974595, 60773035
  - in 'y': 146364022, 243199373, 198022430, 78077248, 59128983, 135006516, 135534747, 81195210, 107349540, 191154276, 155270560, 141213431, 48129895, 249250621, 115169878, 180915260, 171115067, 90354753, 159138663, 133851895, 102531392, 63025520, 51304566

input file used

regions
GRanges object with 9013 ranges and 5 metadata columns:
         seqnames            ranges strand |     value      area   cluster         L  clusterL
            <Rle>         <IRanges>  <Rle> | <numeric> <numeric> <numeric> <numeric> <integer>
     [1]     chr8          75774711      * |  2.949010   2.94901     15171         1         4
     [2]     chr2 51908666-51908808      * |  0.612535   2.45014      7016     27734         4
     [3]     chr3 45240960-45241205      * | -0.448404   3.58723     11459     29451         8
     [4]    chr18 18018893-18019002      * |  0.669870   1.33974      5206     15759         2
     [5]     chr3 52425936-52426038      * | -0.817302   1.63460     11511      6018         2
     ...      ...               ...    ... .       ...       ...       ...       ...       ...
  [9009]    chr22          50902400      * | -0.100129  0.100129      8774         1         1
  [9010]    chr24          22850168      * | -0.100121  0.100121      9363         1         8
  [9011]     chr4          27093075      * | -0.100118  0.100118     12293         1         2
  [9012]    chr11          41409299      * | -0.100041  0.100041      1774         1         3
  [9013]     chr2          73146781      * | -0.100036  0.100036      7167         1         3
  -------

Thank you

lcolladotor commented 2 years ago

Hi @cboschi,

Thanks for the report. Could you share a file with your regions object so I can reproduce the problem? Or make a small example. You might want to use reprex::reprex() for this.

Also, what's your options(width = 120); sessioninfo::session_info() output after getting the error?

Thanks, Leo

cboschi commented 2 years ago

Thank you

Session info 
 version  R version 4.2.1 (2022-06-23 ucrt)
 os       Windows 10 x64 (build 19042)
 system   x86_64, mingw32
 ui       Rgui
 date     2022-08-31
 pandoc   2.19.2 @ C:/Users/.../AppData/Local/Pandoc/ (via rmarkdown)

─ Packages 
 ! package                                      * version   date (UTC) lib source
   affy                                           1.75.0    2022-04-28 [1] Bioconductor
   affyio                                         1.67.0    2022-04-28 [1] Bioconductor
   annotate                                       1.75.0    2022-05-01 [1] Bioconductor
   AnnotationDbi                                * 1.59.1    2022-05-19 [1] Bioconductor
   AnnotationFilter                               1.21.0    2022-04-28 [1] Bioconductor
   askpass                                        1.1       2019-01-13 [1] CRAN (R 4.2.1)
   assertthat                                     0.2.1     2019-03-21 [1] CRAN (R 4.2.1)
   backports                                      1.4.1     2021-12-13 [1] CRAN (R 4.2.0)
   base64                                         2.0.1     2022-08-19 [1] CRAN (R 4.2.1)
   base64enc                                      0.1-3     2015-07-28 [1] CRAN (R 4.2.0)
   beanplot                                       1.3.1     2022-04-09 [1] CRAN (R 4.2.1)
   Biobase                                      * 2.57.1    2022-05-19 [1] Bioconductor
   BiocFileCache                                  2.5.0     2022-04-28 [1] Bioconductor
   BiocGenerics                                 * 0.43.1    2022-07-26 [1] Bioconductor
   BiocIO                                         1.7.1     2022-05-06 [1] Bioconductor
   BiocManager                                    1.30.18   2022-05-18 [1] CRAN (R 4.2.1)
   BiocParallel                                   1.31.12   2022-08-02 [1] Bioconductor
   BiocStyle                                    * 2.25.0    2022-04-28 [1] Bioconductor
   biomaRt                                        2.53.2    2022-05-17 [1] Bioconductor
   Biostrings                                   * 2.65.3    2022-08-25 [1] Bioconductor
   biovizBase                                     1.45.0    2022-05-17 [1] Bioconductor
   bit                                            4.0.4     2020-08-04 [1] CRAN (R 4.2.1)
   bit64                                          4.0.5     2020-08-30 [1] CRAN (R 4.2.1)
   bitops                                         1.0-7     2021-04-24 [1] CRAN (R 4.2.0)
   blob                                           1.2.3     2022-04-10 [1] CRAN (R 4.2.1)
   bookdown                                       0.28.2    2022-08-31 [1] Github (rstudio/bookdown@1bcfd0e)
   BSgenome                                       1.65.2    2022-07-14 [1] Bioconductor
   bslib                                          0.4.0     2022-07-16 [1] CRAN (R 4.2.1)
   bumphunter                                   * 1.39.0    2022-05-17 [1] Bioconductor
   cachem                                         1.0.6     2021-08-19 [1] CRAN (R 4.2.1)
   callr                                          3.7.2     2022-08-22 [1] CRAN (R 4.2.1)
   checkmate                                      2.1.0     2022-04-21 [1] CRAN (R 4.2.1)
   cli                                            3.3.0     2022-04-25 [1] CRAN (R 4.2.1)
   cluster                                        2.1.3     2022-03-28 [2] CRAN (R 4.2.1)
   codetools                                      0.2-18    2020-11-04 [2] CRAN (R 4.2.1)
   colorspace                                     2.0-3     2022-02-21 [1] CRAN (R 4.2.1)
   crayon                                         1.5.1     2022-03-26 [1] CRAN (R 4.2.1)
   curl                                           4.3.2     2021-06-23 [1] CRAN (R 4.2.1)
   data.table                                     1.14.2    2021-09-27 [1] CRAN (R 4.2.1)
   DBI                                            1.1.3     2022-06-18 [1] CRAN (R 4.2.1)
   dbplyr                                         2.2.1     2022-06-27 [1] CRAN (R 4.2.1)
   DEFormats                                      1.25.0    2022-05-04 [1] Bioconductor
   DelayedArray                                   0.23.1    2022-07-28 [1] Bioconductor
   DelayedMatrixStats                             1.19.0    2022-04-28 [1] Bioconductor
   deldir                                         1.0-6     2021-10-23 [1] CRAN (R 4.2.0)
   derfinder                                    * 1.31.0    2022-05-17 [1] Bioconductor
   derfinderHelper                                1.31.0    2022-04-28 [1] Bioconductor
   derfinderPlot                                * 1.31.0    2022-06-08 [1] Bioconductor
   DESeq2                                         1.37.6    2022-08-25 [1] Bioconductor
   dichromat                                      2.0-0.1   2022-05-02 [1] CRAN (R 4.2.0)
   digest                                         0.6.29    2021-12-01 [1] CRAN (R 4.2.1)
   doParallel                                   * 1.0.17    2022-02-07 [1] CRAN (R 4.2.1)
   doRNG                                          1.8.2     2020-01-27 [1] CRAN (R 4.2.1)
   dplyr                                          1.0.9     2022-04-28 [1] CRAN (R 4.2.1)
   DT                                           * 0.24      2022-08-09 [1] CRAN (R 4.2.0)
   edgeR                                          3.39.6    2022-08-07 [1] Bioconductor
   ellipsis                                       0.3.2     2021-04-29 [1] CRAN (R 4.2.1)
   ensembldb                                      2.21.4    2022-08-24 [1] Bioconductor
   evaluate                                       0.16      2022-08-09 [1] CRAN (R 4.2.0)
   fansi                                          1.0.3     2022-03-24 [1] CRAN (R 4.2.1)
   farver                                         2.1.1     2022-07-06 [1] CRAN (R 4.2.1)
   fastmap                                        1.1.0     2021-01-25 [1] CRAN (R 4.2.1)
   FDb.InfiniumMethylation.hg19                 * 2.2.0     2022-08-09 [1] Bioconductor
   filelock                                       1.0.2     2018-10-05 [1] CRAN (R 4.2.1)
   foreach                                      * 1.5.2     2022-02-02 [1] CRAN (R 4.2.1)
   foreign                                        0.8-82    2022-01-16 [2] CRAN (R 4.2.1)
   Formula                                        1.2-4     2020-10-16 [1] CRAN (R 4.2.0)
   genefilter                                     1.79.0    2022-05-01 [1] Bioconductor
   geneplotter                                    1.75.0    2022-05-01 [1] Bioconductor
   generics                                       0.1.3     2022-07-05 [1] CRAN (R 4.2.1)
   GenomeInfoDb                                 * 1.33.5    2022-08-10 [1] Bioconductor
   GenomeInfoDbData                               1.2.8     2022-07-29 [1] Bioconductor
   GenomicAlignments                              1.33.1    2022-07-25 [1] Bioconductor
   GenomicFeatures                              * 1.49.6    2022-08-24 [1] Bioconductor
   GenomicFiles                                   1.33.1    2022-05-17 [1] Bioconductor
   GenomicRanges                                * 1.49.0    2022-04-28 [1] Bioconductor
   GEOquery                                       2.65.2    2022-05-12 [1] Bioconductor
   GGally                                         2.1.2     2021-06-21 [1] CRAN (R 4.2.1)
   ggbio                                        * 1.45.0    2022-06-08 [1] Bioconductor
   ggplot2                                      * 3.3.6     2022-05-03 [1] CRAN (R 4.2.1)
   glue                                           1.6.2     2022-02-24 [1] CRAN (R 4.2.1)
   graph                                          1.75.0    2022-04-28 [1] Bioconductor
   gridExtra                                    * 2.3       2017-09-09 [1] CRAN (R 4.2.1)
   gtable                                         0.3.0     2019-03-25 [1] CRAN (R 4.2.1)
   HDF5Array                                      1.25.2    2022-08-02 [1] Bioconductor
   highr                                          0.9       2021-04-16 [1] CRAN (R 4.2.1)
   Hmisc                                          4.7-1     2022-08-15 [1] CRAN (R 4.2.1)
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   htmlTable                                      2.4.1     2022-07-07 [1] CRAN (R 4.2.1)
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   httr                                           1.4.4     2022-08-17 [1] CRAN (R 4.2.1)
   IlluminaHumanMethylation450kanno.ilmn12.hg19 * 0.6.1     2022-08-02 [1] Bioconductor
   illuminaio                                   * 0.39.0    2022-04-28 [1] Bioconductor
   interp                                         1.1-3     2022-07-13 [1] CRAN (R 4.2.1)
   IRanges                                      * 2.31.2    2022-08-24 [1] Bioconductor
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   jpeg                                           0.1-9     2021-07-24 [1] CRAN (R 4.2.0)
   jquerylib                                      0.1.4     2021-04-26 [1] CRAN (R 4.2.1)
   jsonlite                                       1.8.0     2022-02-22 [1] CRAN (R 4.2.1)
   KEGGREST                                       1.37.3    2022-07-13 [1] Bioconductor
   KernSmooth                                     2.23-20   2021-05-03 [2] CRAN (R 4.2.1)
   knitr                                        * 1.40      2022-08-24 [1] CRAN (R 4.2.1)
   knitrBootstrap                                 1.0.2     2018-05-24 [1] CRAN (R 4.2.1)
   labeling                                       0.4.2     2020-10-20 [1] CRAN (R 4.2.0)
   lattice                                        0.20-45   2021-09-22 [2] CRAN (R 4.2.1)
   latticeExtra                                   0.6-30    2022-07-04 [1] CRAN (R 4.2.1)
   lazyeval                                       0.2.2     2019-03-15 [1] CRAN (R 4.2.1)
   lifecycle                                      1.0.1     2021-09-24 [1] CRAN (R 4.2.1)
   limma                                        * 3.53.6    2022-08-24 [1] Bioconductor
   locfit                                       * 1.5-9.6   2022-07-11 [1] CRAN (R 4.2.1)
   lubridate                                      1.8.0     2021-10-07 [1] CRAN (R 4.2.1)
   lumi                                         * 2.49.0    2022-05-17 [1] Bioconductor
   magrittr                                       2.0.3     2022-03-30 [1] CRAN (R 4.2.1)
   markdown                                     * 1.1       2019-08-07 [1] CRAN (R 4.2.1)
   MASS                                           7.3-58.1  2022-08-03 [1] CRAN (R 4.2.1)
   Matrix                                         1.4-1     2022-03-23 [2] CRAN (R 4.2.1)
   MatrixGenerics                               * 1.9.1     2022-06-29 [1] Bioconductor
   matrixStats                                  * 0.62.0    2022-04-19 [1] CRAN (R 4.2.1)
   mclust                                         5.4.10    2022-05-20 [1] CRAN (R 4.2.1)
   memoise                                        2.0.1     2021-11-26 [1] CRAN (R 4.2.1)
   methylumi                                    * 2.43.0    2022-05-17 [1] Bioconductor
   mgcv                                         * 1.8-40    2022-03-29 [2] CRAN (R 4.2.1)
   minfi                                        * 1.43.0    2022-05-17 [1] Bioconductor
   multtest                                       2.53.0    2022-04-28 [1] Bioconductor
   munsell                                        0.5.0     2018-06-12 [1] CRAN (R 4.2.1)
   nleqslv                                        3.3.3     2022-08-07 [1] CRAN (R 4.2.1)
   nlme                                         * 3.1-159   2022-08-09 [1] CRAN (R 4.2.1)
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   nor1mix                                        1.3-0     2019-06-13 [1] CRAN (R 4.2.1)
   openssl                                        2.0.2     2022-05-24 [1] CRAN (R 4.2.1)
   org.Hs.eg.db                                 * 3.15.0    2022-08-09 [1] Bioconductor
   OrganismDbi                                    1.39.1    2022-06-08 [1] Bioconductor
   pillar                                         1.8.1     2022-08-19 [1] CRAN (R 4.2.1)
   pkgbuild                                       1.3.1     2021-12-20 [1] CRAN (R 4.2.1)
   pkgconfig                                      2.0.3     2019-09-22 [1] CRAN (R 4.2.1)
   plyr                                           1.8.7     2022-03-24 [1] CRAN (R 4.2.1)
   png                                            0.1-7     2013-12-03 [1] CRAN (R 4.2.0)
   preprocessCore                                 1.59.0    2022-04-28 [1] Bioconductor
   prettyunits                                    1.1.1     2020-01-24 [1] CRAN (R 4.2.1)
   processx                                       3.7.0     2022-07-07 [1] CRAN (R 4.2.1)
   progress                                       1.2.2     2019-05-16 [1] CRAN (R 4.2.1)
   ProtGenerics                                   1.29.0    2022-04-28 [1] Bioconductor
   ps                                             1.7.1     2022-06-18 [1] CRAN (R 4.2.1)
   purrr                                          0.3.4     2020-04-17 [1] CRAN (R 4.2.1)
   quadprog                                       1.5-8     2019-11-20 [1] CRAN (R 4.2.0)
   qvalue                                         2.29.0    2022-04-28 [1] Bioconductor
   R6                                             2.5.1     2021-08-19 [1] CRAN (R 4.2.1)
   rappdirs                                       0.3.3     2021-01-31 [1] CRAN (R 4.2.1)
   RBGL                                           1.73.0    2022-04-28 [1] Bioconductor
   RColorBrewer                                 * 1.1-3     2022-04-03 [1] CRAN (R 4.2.0)
   Rcpp                                           1.0.9     2022-07-08 [1] CRAN (R 4.2.1)
   RCurl                                          1.98-1.8  2022-07-30 [1] CRAN (R 4.2.1)
   readr                                          2.1.2     2022-01-30 [1] CRAN (R 4.2.1)
   RefManageR                                     1.3.5     2022-08-31 [1] Github (ropensci/RefManageR@3b30bc6)
   regionReport                                 * 1.31.0    2022-05-17 [1] Bioconductor
   remotes                                        2.4.2     2021-11-30 [1] CRAN (R 4.2.1)
   reshape                                        0.8.9     2022-04-12 [1] CRAN (R 4.2.1)
   reshape2                                     * 1.4.4     2020-04-09 [1] CRAN (R 4.2.1)
   restfulr                                       0.0.15    2022-06-16 [1] CRAN (R 4.2.1)
   rhdf5                                          2.41.1    2022-06-21 [1] Bioconductor
 D rhdf5filters                                   1.9.0     2022-04-28 [1] Bioconductor
   Rhdf5lib                                       1.19.2    2022-05-13 [1] Bioconductor
   rjson                                          0.2.21    2022-01-09 [1] CRAN (R 4.2.0)
   rlang                                          1.0.4     2022-07-12 [1] CRAN (R 4.2.1)
   rmarkdown                                      2.16.1    2022-08-31 [1] Github (rstudio/rmarkdown@b8a9879)
   rngtools                                       1.5.2     2021-09-20 [1] CRAN (R 4.2.1)
   ROC                                          * 1.73.0    2022-04-28 [1] Bioconductor
   rpart                                          4.1.16    2022-01-24 [2] CRAN (R 4.2.1)
   rprojroot                                      2.0.3     2022-04-02 [1] CRAN (R 4.2.1)
   Rsamtools                                      2.13.4    2022-08-24 [1] Bioconductor
   RSQLite                                        2.2.16    2022-08-17 [1] CRAN (R 4.2.1)
   rstudioapi                                     0.14      2022-08-22 [1] CRAN (R 4.2.1)
   rtracklayer                                    1.57.0    2022-05-12 [1] Bioconductor
   S4Vectors                                    * 0.35.1    2022-06-08 [1] Bioconductor
   sass                                           0.4.2     2022-07-16 [1] CRAN (R 4.2.1)
   scales                                       * 1.2.1     2022-08-20 [1] CRAN (R 4.2.1)
   scrime                                         1.3.5     2018-12-01 [1] CRAN (R 4.2.1)
   sessioninfo                                  * 1.2.2     2021-12-06 [1] CRAN (R 4.2.1)
   siggenes                                       1.71.0    2022-04-28 [1] Bioconductor
   sparseMatrixStats                              1.9.0     2022-04-28 [1] Bioconductor
   stringi                                        1.7.8     2022-07-11 [1] CRAN (R 4.2.1)
   stringr                                        1.4.1     2022-08-20 [1] CRAN (R 4.2.1)
   SummarizedExperiment                         * 1.27.2    2022-08-24 [1] Bioconductor
   survival                                       3.3-1     2022-03-03 [2] CRAN (R 4.2.1)
   tibble                                         3.1.8     2022-07-22 [1] CRAN (R 4.2.1)
   tidyr                                          1.2.0     2022-02-01 [1] CRAN (R 4.2.1)
   tidyselect                                     1.1.2     2022-02-21 [1] CRAN (R 4.2.1)
   TxDb.Hsapiens.UCSC.hg19.knownGene            * 3.2.2     2022-08-09 [1] Bioconductor
   tzdb                                           0.3.0     2022-03-28 [1] CRAN (R 4.2.1)
   utf8                                           1.2.2     2021-07-24 [1] CRAN (R 4.2.1)
   VariantAnnotation                              1.43.3    2022-08-14 [1] Bioconductor
   vctrs                                          0.4.1     2022-04-13 [1] CRAN (R 4.2.1)
   wateRmelon                                   * 2.3.0     2022-05-17 [1] Bioconductor
   whisker                                      * 0.4       2019-08-28 [1] CRAN (R 4.2.1)
   withr                                          2.5.0     2022-03-03 [1] CRAN (R 4.2.1)
   xfun                                           0.32      2022-08-10 [1] CRAN (R 4.2.1)
   XML                                            3.99-0.10 2022-06-09 [1] CRAN (R 4.2.0)
   xml2                                           1.3.3     2021-11-30 [1] CRAN (R 4.2.1)
   xtable                                         1.8-4     2019-04-21 [1] CRAN (R 4.2.1)
   XVector                                      * 0.37.1    2022-08-25 [1] Bioconductor
   yaml                                           2.3.5     2022-02-21 [1] CRAN (R 4.2.0)
   zlibbioc                                       1.43.0    2022-04-28 [1] Bioconductor

 D ── DLL MD5 mismatch, broken installation.
lcolladotor commented 2 years ago

Thanks, I see that you are using bioc-devel then. Can you share your regions file then? Or a subset of it that reproduces the issue? Thanks!

I suspect that the error is related to the txdb argument and https://github.com/leekgroup/regionReport/blob/8c39b21cd4255b6aebb7b38262c6a65c07a3fa96/R/renderReport.R#L307. Like, your regions object might on hg38 coordinates instead of hg19. You could try with txdb = TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene.

Likely if you run seqlengths(regions) and seqlengths(TxDb.Hsapiens.UCSC.hg19.knownGene) you might see the numbers you see above. 

  sequences chr8, chr2, chr3, chr18, chr19, chr11, chr10, chr17, chr14, chr4, chrX, chr9, chr21, chr1, chr13, chr5, chr6, chr16, chr7, chr12, chr15, chr20, chr22 have incompatible seqlengths:
  - in 'x': 113319770, 136231102, 121005158, 65820629, 63449741, 106982474, 103308737, 73167244, 82403003, 120000601, 139009144, 105454467, 69862954, 158534110, 83472345, 120089316, 117806340, 81013979, 110682743, 87216183, 85007780, 71974595, 60773035
  - in 'y': 146364022, 243199373, 198022430, 78077248, 59128983, 135006516, 135534747, 81195210, 107349540, 191154276, 155270560, 141213431, 48129895, 249250621, 115169878, 180915260, 171115067, 90354753, 159138663, 133851895, 102531392, 63025520, 51304566

Best, Leo

cboschi commented 2 years ago 
example <- new("GRanges", seqnames = new("Rle", values = structure(c(1L, 
2L, 3L, 4L, 2L), levels = c("chr8", "chr3", "chr2", "chr26", 
"chr4", "chr1", "chr19", "chr18", "chr24", "chr20", "chrX", "chr21", 
"chr10", "chr7", "chr22", "chr16", "chr11", "chr28", "chr23", 
"chr17", "chr25", "chr9", "chr14"), class = "factor"), lengths = c(1L, 
1L, 1L, 1L, 1L), elementMetadata = NULL, metadata = list()), 
    ranges = new("IRanges", start = c(75774711L, 106589999L, 
    51908767L, 19225812L, 2713703L), width = c(1L, 1L, 1L, 1L, 
    24L), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, 
        metadata = list()), strand = new("Rle", values = structure(3L, levels = c("+", 
    "-", "*"), class = "factor"), lengths = 5L, elementMetadata = NULL, 
     metadata = list()), seqinfo = new("Seqinfo", seqnames = c("chr8", 
    "chr3", "chr2", "chr26", "chr4", "chr1", "chr19", "chr18", 
    "chr24", "chr20", "chrX", "chr21", "chr10", "chr7", "chr22", 
    "chr16", "chr11", "chr28", "chr23", "chr17", "chr25", "chr9", 
    "chr14"), seqlengths = c(113319770L, 121005158L, 136231102L, 
    51992305L, 120000601L, 158534110L, 63449741L, 65820629L, 
    62317253L, 71974595L, 139009144L, 69862954L, 103308737L, 
    110682743L, 60773035L, 81013979L, 106982474L, 45940150L, 
    52498615L, 73167244L, 42350435L, 105454467L, 82403003L), 
        is_circular = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
        NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA), 
        genome = c(NA_character_, NA_character_, NA_character_, 
        NA_character_, NA_character_, NA_character_, NA_character_, 
        NA_character_, NA_character_, NA_character_, NA_character_, 
        NA_character_, NA_character_, NA_character_, NA_character_, 
        NA_character_, NA_character_, NA_character_, NA_character_, 
        NA_character_, NA_character_, NA_character_, NA_character_
        )), elementMetadata = new("DFrame", rownames = NULL, 
      nrows = 5L, elementType = "ANY", elementMetadata = NULL, 
      metadata = list(), listData = list(value = c(2.94901017596346, 
      -2.34900730540258, 1.92517410632881, 1.73928126017044, 
      -0.809506533946836), area = c(2.94901017596346, 2.34900730540258, 
      1.92517410632881, 1.73928126017044, 1.61901306789367), 
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     1, 1, 1, 1098), clusterL = c(4L, 1L, 4L, 6L, 5L))), 
    elementType = "ANY", metadata = list())
cboschi commented 2 years ago

Thank you Leo, the issue was about the txdb argument. I added the cattle annotation and it worked, see the code below.

report <- renderReport(example, "Example bumphunter", pvalueVars = NULL, 
densityVars = c("Area" = "area", "Value" = "value", "Cluster Length" = "clusterL"), 
significantVar = NULL, output = "report", outdir = "report", device = "png", txdb = TxDb.Btaurus.UCSC.bosTau9.refGene)
lcolladotor commented 2 years ago

Awesome! I'm glad to hear that it's working now. Have a good day =)