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recount::getTPM(rse) method #30

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SoniaRuiz opened this issue Jan 16, 2023 · 2 comments
Open
1 task

recount::getTPM(rse) method #30

SoniaRuiz opened this issue Jan 16, 2023 · 2 comments
Labels
bug Something isn't working
Milestone
bioc v3.20

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@SoniaRuiz
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Description of the issue

The function "recount::getTPM(rse)" returns the unexpected error message: 'Error: subscript contains invalid names'.

Below, is a reproducible example that I have been using:

rse <- recount3::create_rse_manual(
      project = "BLOOD",
      project_home = "data_sources/gtex",
      organism = "human",
      annotation = "gencode_v29",
      type = "gene")

SummarizedExperiment::assays(rse)$counts <- recount3::transform_counts(rse)
SummarizedExperiment::assays(rse)$TPM <- recount::getTPM(rse)

When I look at the 'rowData(rse)' dimension of the object 'rse', I cannot see the column name 'bp_length':

> rowData(rse) %>% names
 [1] "source"      "type"        "score"       "phase"       "gene_id"     "gene_type"   "gene_name"   "level"       "havana_gene" "tag"

Maybe that's the issue?

Expected behavior

The function 'recount::getTPM(rse)' to return the gene-level TPM values across the samples of the project provided on the function 'recount3::create_rse_manual()', as it is reported on https://rdrr.io/bioc/recount/man/getTPM.html.

R Session Information

Below is the output of sessioninfo::session_info().

> sessioninfo::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.5 (2021-03-31)
 os       Ubuntu 16.04.7 LTS          
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_GB.UTF-8                 
 ctype    en_GB.UTF-8                 
 tz       Europe/London               
 date     2023-01-16                  

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version  date       lib source        
 AnnotationDbi          1.52.0   2020-10-27 [2] Bioconductor  
 askpass                1.1      2019-01-13 [2] CRAN (R 4.0.5)
 assertthat             0.2.1    2019-03-21 [2] CRAN (R 4.0.5)
 backports              1.2.1    2020-12-09 [2] CRAN (R 4.0.5)
 base64enc              0.1-3    2015-07-28 [2] CRAN (R 4.0.5)
 Biobase              * 2.50.0   2020-10-27 [2] Bioconductor  
 BiocFileCache          1.14.0   2020-10-27 [2] Bioconductor  
 BiocGenerics         * 0.36.1   2021-04-16 [2] Bioconductor  
 BiocParallel           1.24.1   2020-11-06 [2] Bioconductor  
 biomaRt                2.46.3   2021-02-09 [2] Bioconductor  
 Biostrings             2.58.0   2020-10-27 [2] Bioconductor  
 bit                    4.0.4    2020-08-04 [2] CRAN (R 4.0.5)
 bit64                  4.0.5    2020-08-30 [2] CRAN (R 4.0.5)
 bitops                 1.0-7    2021-04-24 [2] CRAN (R 4.0.5)
 blob                   1.2.2    2021-07-23 [2] CRAN (R 4.0.5)
 BSgenome               1.58.0   2020-10-27 [1] Bioconductor  
 bumphunter             1.32.0   2020-10-27 [1] Bioconductor  
 cachem                 1.0.6    2021-08-19 [1] CRAN (R 4.0.5)
 checkmate              2.0.0    2020-02-06 [1] CRAN (R 4.0.5)
 cli                    3.0.1    2021-07-17 [1] CRAN (R 4.0.5)
 cluster                2.1.2    2021-04-17 [2] CRAN (R 4.0.5)
 codetools              0.2-18   2020-11-04 [2] CRAN (R 4.0.5)
 colorspace             2.0-2    2021-06-24 [2] CRAN (R 4.0.5)
 crayon                 1.4.1    2021-02-08 [2] CRAN (R 4.0.5)
 curl                   4.3.2    2021-06-23 [2] CRAN (R 4.0.5)
 data.table             1.14.0   2021-02-21 [2] CRAN (R 4.0.5)
 DBI                    1.1.1    2021-01-15 [2] CRAN (R 4.0.5)
 dbplyr                 2.1.1    2021-04-06 [2] CRAN (R 4.0.5)
 DelayedArray           0.16.3   2021-03-24 [2] Bioconductor  
 derfinder              1.24.2   2020-12-18 [1] Bioconductor  
 derfinderHelper        1.24.1   2020-12-18 [1] Bioconductor  
 digest                 0.6.27   2020-10-24 [2] CRAN (R 4.0.5)
 doRNG                  1.8.2    2020-01-27 [1] CRAN (R 4.0.5)
 downloader             0.4      2015-07-09 [1] CRAN (R 4.0.5)
 dplyr                  1.0.7    2021-06-18 [2] CRAN (R 4.0.5)
 ellipsis               0.3.2    2021-04-29 [2] CRAN (R 4.0.5)
 fansi                  0.5.0    2021-05-25 [2] CRAN (R 4.0.5)
 fastmap                1.1.0    2021-01-25 [2] CRAN (R 4.0.5)
 foreach                1.5.1    2020-10-15 [2] CRAN (R 4.0.5)
 foreign                0.8-81   2020-12-22 [2] CRAN (R 4.0.5)
 Formula                1.2-4    2020-10-16 [1] CRAN (R 4.0.5)
 generics               0.1.0    2020-10-31 [2] CRAN (R 4.0.5)
 GenomeInfoDb         * 1.26.7   2021-04-08 [2] Bioconductor  
 GenomeInfoDbData       1.2.4    2021-07-03 [2] Bioconductor  
 GenomicAlignments      1.26.0   2020-10-27 [2] Bioconductor  
 GenomicFeatures        1.42.3   2021-04-01 [1] Bioconductor  
 GenomicFiles           1.26.0   2020-10-27 [1] Bioconductor  
 GenomicRanges        * 1.42.0   2020-10-27 [2] Bioconductor  
 GEOquery               2.58.0   2020-10-27 [1] Bioconductor  
 ggplot2                3.3.5    2021-06-25 [2] CRAN (R 4.0.5)
 glue                   1.4.2    2020-08-27 [2] CRAN (R 4.0.5)
 gridExtra              2.3      2017-09-09 [2] CRAN (R 4.0.5)
 gtable                 0.3.0    2019-03-25 [2] CRAN (R 4.0.5)
 Hmisc                  4.6-0    2021-10-07 [1] CRAN (R 4.0.5)
 hms                    1.1.0    2021-05-17 [2] CRAN (R 4.0.5)
 htmlTable              2.3.0    2021-10-12 [1] CRAN (R 4.0.5)
 htmltools              0.5.1.1  2021-01-22 [2] CRAN (R 4.0.5)
 htmlwidgets            1.5.3    2020-12-10 [2] CRAN (R 4.0.5)
 httr                   1.4.2    2020-07-20 [2] CRAN (R 4.0.5)
 IRanges              * 2.24.1   2020-12-12 [2] Bioconductor  
 iterators              1.0.13   2020-10-15 [2] CRAN (R 4.0.5)
 jpeg                   0.1-9    2021-07-24 [1] CRAN (R 4.0.5)
 jsonlite               1.7.2    2020-12-09 [2] CRAN (R 4.0.5)
 knitr                  1.34     2021-09-09 [1] CRAN (R 4.0.5)
 lattice                0.20-44  2021-05-02 [2] CRAN (R 4.0.5)
 latticeExtra           0.6-29   2019-12-19 [1] CRAN (R 4.0.5)
 lifecycle              1.0.0    2021-02-15 [2] CRAN (R 4.0.5)
 limma                  3.46.0   2020-10-27 [2] Bioconductor  
 locfit                 1.5-9.4  2020-03-25 [2] CRAN (R 4.0.5)
 magrittr               2.0.1    2020-11-17 [2] CRAN (R 4.0.5)
 Matrix                 1.3-4    2021-06-01 [2] CRAN (R 4.0.5)
 MatrixGenerics       * 1.2.1    2021-01-30 [2] Bioconductor  
 matrixStats          * 0.60.1   2021-08-23 [1] CRAN (R 4.0.5)
 memoise                2.0.0    2021-01-26 [2] CRAN (R 4.0.5)
 munsell                0.5.0    2018-06-12 [2] CRAN (R 4.0.5)
 nnet                   7.3-16   2021-05-03 [2] CRAN (R 4.0.5)
 openssl                1.4.5    2021-09-02 [1] CRAN (R 4.0.5)
 pillar                 1.6.2    2021-07-29 [2] CRAN (R 4.0.5)
 pkgconfig              2.0.3    2019-09-22 [2] CRAN (R 4.0.5)
 plyr                   1.8.6    2020-03-03 [2] CRAN (R 4.0.5)
 png                    0.1-7    2013-12-03 [1] CRAN (R 4.0.5)
 prettyunits            1.1.1    2020-01-24 [2] CRAN (R 4.0.5)
 progress               1.2.2    2019-05-16 [2] CRAN (R 4.0.5)
 purrr                  0.3.4    2020-04-17 [2] CRAN (R 4.0.5)
 qvalue                 2.22.0   2020-10-27 [1] Bioconductor  
 R.methodsS3            1.8.1    2020-08-26 [1] CRAN (R 4.0.5)
 R.oo                   1.24.0   2020-08-26 [1] CRAN (R 4.0.5)
 R.utils                2.10.1   2020-08-26 [1] CRAN (R 4.0.5)
 R6                     2.5.1    2021-08-19 [1] CRAN (R 4.0.5)
 rappdirs               0.3.3    2021-01-31 [2] CRAN (R 4.0.5)
 RColorBrewer           1.1-2    2014-12-07 [2] CRAN (R 4.0.5)
 Rcpp                   1.0.7    2021-07-07 [1] CRAN (R 4.0.5)
 RCurl                  1.98-1.4 2021-08-17 [1] CRAN (R 4.0.5)
 readr                  2.0.1    2021-08-10 [1] CRAN (R 4.0.5)
 recount              * 1.16.1   2020-12-18 [1] Bioconductor  
 recount3             * 1.0.7    2021-02-11 [1] Bioconductor  
 rentrez                1.2.3    2020-11-10 [1] CRAN (R 4.0.5)
 reshape2               1.4.4    2020-04-09 [2] CRAN (R 4.0.5)
 rlang                  1.0.6    2022-09-24 [1] CRAN (R 4.0.5)
 rngtools               1.5.2    2021-09-20 [1] CRAN (R 4.0.5)
 rpart                  4.1-15   2019-04-12 [2] CRAN (R 4.0.5)
 Rsamtools              2.6.0    2020-10-27 [2] Bioconductor  
 RSQLite                2.2.8    2021-08-21 [1] CRAN (R 4.0.5)
 rstudioapi             0.13     2020-11-12 [2] CRAN (R 4.0.5)
 rtracklayer            1.50.0   2020-10-27 [2] Bioconductor  
 S4Vectors            * 0.28.1   2020-12-09 [2] Bioconductor  
 scales                 1.1.1    2020-05-11 [2] CRAN (R 4.0.5)
 sessioninfo            1.1.1    2018-11-05 [2] CRAN (R 4.0.5)
 stringi                1.7.4    2021-08-25 [1] CRAN (R 4.0.5)
 stringr                1.4.0    2019-02-10 [2] CRAN (R 4.0.5)
 SummarizedExperiment * 1.20.0   2020-10-27 [2] Bioconductor  
 survival               3.2-13   2021-08-24 [1] CRAN (R 4.0.5)
 tibble                 3.1.4    2021-08-25 [1] CRAN (R 4.0.5)
 tidyr                  1.1.3    2021-03-03 [2] CRAN (R 4.0.5)
 tidyselect             1.1.1    2021-04-30 [2] CRAN (R 4.0.5)
 tzdb                   0.1.2    2021-07-20 [2] CRAN (R 4.0.5)
 utf8                   1.2.2    2021-07-24 [2] CRAN (R 4.0.5)
 VariantAnnotation      1.36.0   2020-10-27 [1] Bioconductor  
 vctrs                  0.3.8    2021-04-29 [2] CRAN (R 4.0.5)
 withr                  2.4.2    2021-04-18 [2] CRAN (R 4.0.5)
 xfun                   0.25     2021-08-06 [1] CRAN (R 4.0.5)
 XML                    3.99-0.7 2021-08-17 [1] CRAN (R 4.0.5)
 xml2                   1.3.2    2020-04-23 [2] CRAN (R 4.0.5)
 XVector                0.30.0   2020-10-27 [2] Bioconductor  
 yaml                   2.2.1    2020-02-01 [2] CRAN (R 4.0.5)
 zlibbioc               1.36.0   2020-10-27 [2] Bioconductor  

[1] /home/sruiz/R/x86_64-pc-linux-gnu-library/4.0
[2] /opt/R/4.0.5/lib/R/library

Indicate whether BiocManager::valid() returns TRUE.

  • BiocManager::valid() is TRUE
> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

* sessionInfo()

R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.7 LTS

Matrix products: default
BLAS:   /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

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    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] recount_1.16.1              recount3_1.0.7              SummarizedExperiment_1.20.0 Biobase_2.50.0              GenomicRanges_1.42.0        GenomeInfoDb_1.26.7        
 [7] IRanges_2.24.1              S4Vectors_0.28.1            BiocGenerics_0.36.1         MatrixGenerics_1.2.1        matrixStats_0.60.1         

loaded via a namespace (and not attached):
  [1] colorspace_2.0-2         ellipsis_0.3.2           qvalue_2.22.0            htmlTable_2.3.0          XVector_0.30.0           base64enc_0.1-3          rstudioapi_0.13         
  [8] bit64_4.0.5              AnnotationDbi_1.52.0     fansi_0.5.0              xml2_1.3.2               codetools_0.2-18         splines_4.0.5            R.methodsS3_1.8.1       
 [15] cachem_1.0.6             knitr_1.34               jsonlite_1.7.2           Formula_1.2-4            Rsamtools_2.6.0          cluster_2.1.2            dbplyr_2.1.1            
 [22] png_0.1-7                R.oo_1.24.0              BiocManager_1.30.16      rentrez_1.2.3            readr_2.0.1              compiler_4.0.5           httr_1.4.2              
 [29] backports_1.2.1          assertthat_0.2.1         Matrix_1.3-4             fastmap_1.1.0            limma_3.46.0             cli_3.0.1                htmltools_0.5.1.1       
 [36] prettyunits_1.1.1        tools_4.0.5              gtable_0.3.0             glue_1.4.2               GenomeInfoDbData_1.2.4   reshape2_1.4.4           dplyr_1.0.7             
 [43] doRNG_1.8.2              rappdirs_0.3.3           Rcpp_1.0.7               bumphunter_1.32.0        vctrs_0.3.8              Biostrings_2.58.0        rtracklayer_1.50.0      
 [50] iterators_1.0.13         xfun_0.25                stringr_1.4.0            lifecycle_1.0.0          rngtools_1.5.2           XML_3.99-0.7             zlibbioc_1.36.0         
 [57] scales_1.1.1             BSgenome_1.58.0          VariantAnnotation_1.36.0 hms_1.1.0                GEOquery_2.58.0          derfinderHelper_1.24.1   RColorBrewer_1.1-2      
 [64] yaml_2.2.1               curl_4.3.2               memoise_2.0.0            gridExtra_2.3            downloader_0.4           ggplot2_3.3.5            biomaRt_2.46.3          
 [71] rpart_4.1-15             latticeExtra_0.6-29      stringi_1.7.4            RSQLite_2.2.8            foreach_1.5.1            checkmate_2.0.0          GenomicFeatures_1.42.3  
 [78] BiocParallel_1.24.1      rlang_1.0.6              pkgconfig_2.0.3          GenomicFiles_1.26.0      bitops_1.0-7             lattice_0.20-44          purrr_0.3.4             
 [85] GenomicAlignments_1.26.0 htmlwidgets_1.5.3        bit_4.0.4                tidyselect_1.1.1         plyr_1.8.6               magrittr_2.0.1           R6_2.5.1                
 [92] generics_0.1.0           Hmisc_4.6-0              DelayedArray_0.16.3      DBI_1.1.1                pillar_1.6.2             foreign_0.8-81           withr_2.4.2             
 [99] survival_3.2-13          RCurl_1.98-1.4           nnet_7.3-16              tibble_3.1.4             crayon_1.4.1             derfinder_1.24.2         utf8_1.2.2              
[106] BiocFileCache_1.14.0     tzdb_0.1.2               jpeg_0.1-9               progress_1.2.2           locfit_1.5-9.4           grid_4.0.5               data.table_1.14.0       
[113] blob_1.2.2               digest_0.6.27            tidyr_1.1.3              R.utils_2.10.1           openssl_1.4.5            munsell_0.5.0            sessioninfo_1.1.1       
[120] askpass_1.1             

Bioconductor version '3.12'

  * 246 packages out-of-date
  * 1 packages too new

create a valid installation with

  BiocManager::install(c(
    "backports", "bayestestR", "BH", "BiocManager", "bit", "blob", "bookdown", "brew", "brio", "broom", "broom.mixed", "bslib", "cachem", "Cairo", "callr", "car", "carData", "checkmate", "classInt",
    "cli", "clipr", "coloc", "colorRamps", "colorspace", "commonmark", "conquer", "corrplot", "covr", "cpp11", "crayon", "credentials", "crosstalk", "curl", "dasper", "data.table", "datawizard",
    "DBI", "DBItest", "dbplyr", "deldir", "desc", "devtools", "diffobj", "digest", "doParallel", "doRNG", "dplyr", "DT", "dtplyr", "e1071", "effectsize", "estimability", "evaluate", "extrafont",
    "fansi", "farver", "fdrtool", "filehash", "fontawesome", "forcats", "foreach", "formatR", "fs", "gargle", "generics", "gert", "ggbeeswarm", "ggeffects", "ggforce", "ggplot2", "ggpubr",
    "ggrastr", "ggrepel", "ggsignif", "ggstance", "gh", "gitcreds", "glue", "googlesheets4", "gplots", "gprofiler2", "gtable", "gtools", "haven", "highr", "Hmisc", "hms", "htmlTable", "htmltools",
    "htmlwidgets", "httpuv", "httr", "insight", "irlba", "isoband", "iterators", "jpeg", "jsonlite", "jtools", "knitr", "later", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maps",
    "maptools", "markdown", "MatrixModels", "matrixStats", "memoise", "mime", "minqa", "mixsqp", "modelr", "mvtnorm", "nloptr", "openssl", "openxlsx", "packrat", "pander", "parameters", "pbapply",
    "performance", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "png", "polyclip", "polynom", "processx", "proj4", "proxy", "ps", "purrr", "quantreg", "R.methodsS3", "R.oo", "R.utils", "R6",
    "ragg", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "RefManageR", "remotes", "reprex", "reshape", "reticulate", "rex", "rio", "rJava", "rjson",
    "rlang", "rmarkdown", "roxygen2", "rprojroot", "rsconnect", "RSQLite", "rstatix", "rstudioapi", "Rttf2pt1", "rversions", "rvest", "s2", "sandwich", "sass", "scales", "sessioninfo", "shiny",
    "shinyBS", "shinydashboard", "shinyjs", "sjlabelled", "sjmisc", "sjPlot", "sjstats", "snow", "sp", "statmod", "stringi", "stringr", "susieR", "svglite", "sys", "systemfonts", "testthat",
    "textshaping", "tibble", "tidyr", "tidyselect", "tidyverse", "tinytex", "transport", "tweenr", "tzdb", "usethis", "uuid", "V8", "vctrs", "viridis", "viridisLite", "vroom", "waldo", "webshot",
    "whisker", "withr", "wk", "xfun", "XML", "xml2", "yaml", "zip", "zoo"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Is the package installed via bioconda?

NO
@lcolladotor
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Hm.... http://research.libd.org/recount3/reference/transform_counts.html shows a working case where computing TPMs does work.

Also, using your example R code I couldn't reproduce the issue:

devel > rse <- recount3::create_rse_manual(
+       project = "BLOOD",
+       project_home = "data_sources/gtex",
+       organism = "human",
+       annotation = "gencode_v29",
+       type = "gene")
2023-05-06 19:54:15.455204 downloading and reading the metadata.
2023-05-06 19:54:15.899823 caching file gtex.gtex.BLOOD.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/OD/BLOOD/gtex.gtex.BLOOD.MD.gz'
  |=================================================================================| 100%

2023-05-06 19:54:17.301443 caching file gtex.recount_project.BLOOD.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/OD/BLOOD/gtex.recount_project.BLOOD.MD.gz'
  |=================================================================================| 100%

2023-05-06 19:54:18.317409 caching file gtex.recount_qc.BLOOD.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/OD/BLOOD/gtex.recount_qc.BLOOD.MD.gz'
  |=================================================================================| 100%

2023-05-06 19:54:19.555473 caching file gtex.recount_seq_qc.BLOOD.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/OD/BLOOD/gtex.recount_seq_qc.BLOOD.MD.gz'
  |=================================================================================| 100%

2023-05-06 19:54:20.419423 downloading and reading the feature information.
2023-05-06 19:54:20.787712 caching file human.gene_sums.G029.gtf.gz.
adding rname 'http://duffel.rail.bio/recount3/human/annotations/gene_sums/human.gene_sums.G029.gtf.gz'
  |=================================================================================| 100%

2023-05-06 19:54:22.512853 downloading and reading the counts: 1048 samples across 64837 features.
2023-05-06 19:54:22.94642 caching file gtex.gene_sums.BLOOD.G029.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/gene_sums/OD/BLOOD/gtex.gene_sums.BLOOD.G029.gz'
  |=================================================================================| 100%

2023-05-06 19:54:40.040121 constructing the RangedSummarizedExperiment (rse) object.
devel > 
devel > SummarizedExperiment::assays(rse)$counts <- recount3::transform_counts(rse)
devel > SummarizedExperiment::assays(rse)$TPM <- recount::getTPM(rse)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
devel > options(width = 120)
devel > sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.0 (2023-04-21)
 os       macOS Ventura 13.0.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2023-05-06
 rstudio  2023.03.0+386 Cherry Blossom (desktop)
 pandoc   2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 AnnotationDbi          1.62.1    2023-05-02 [1] Bioconductor
 backports              1.4.1     2021-12-13 [1] CRAN (R 4.3.0)
 base64enc              0.1-3     2015-07-28 [1] CRAN (R 4.3.0)
 Biobase                2.60.0    2023-04-25 [1] Bioconductor
 BiocFileCache          2.8.0     2023-04-25 [1] Bioconductor
 BiocGenerics           0.46.0    2023-04-25 [1] Bioconductor
 BiocIO                 1.10.0    2023-04-25 [1] Bioconductor
 BiocParallel           1.34.0    2023-04-25 [1] Bioconductor
 biocthis               1.11.1    2023-05-06 [1] Github (lcolladotor/biocthis@42dc8df)
 biomaRt                2.56.0    2023-04-25 [1] Bioconductor
 Biostrings             2.68.0    2023-04-25 [1] Bioconductor
 bit                    4.0.5     2022-11-15 [1] CRAN (R 4.3.0)
 bit64                  4.0.5     2020-08-30 [1] CRAN (R 4.3.0)
 bitops                 1.0-7     2021-04-24 [1] CRAN (R 4.3.0)
 blob                   1.2.4     2023-03-17 [1] CRAN (R 4.3.0)
 brio                   1.1.3     2021-11-30 [1] CRAN (R 4.3.0)
 BSgenome               1.68.0    2023-04-25 [1] Bioconductor
 bumphunter             1.42.0    2023-04-25 [1] Bioconductor
 cachem                 1.0.8     2023-05-01 [1] CRAN (R 4.3.0)
 callr                  3.7.3     2022-11-02 [1] CRAN (R 4.3.0)
 checkmate              2.2.0     2023-04-27 [1] CRAN (R 4.3.0)
 cli                    3.6.1     2023-03-23 [1] CRAN (R 4.3.0)
 cluster                2.1.4     2022-08-22 [1] CRAN (R 4.3.0)
 codetools              0.2-19    2023-02-01 [1] CRAN (R 4.3.0)
 colorout               1.2-2     2023-05-06 [1] Github (jalvesaq/colorout@79931fd)
 colorspace             2.1-0     2023-01-23 [1] CRAN (R 4.3.0)
 crayon                 1.5.2     2022-09-29 [1] CRAN (R 4.3.0)
 curl                   5.0.0     2023-01-12 [1] CRAN (R 4.3.0)
 data.table             1.14.8    2023-02-17 [1] CRAN (R 4.3.0)
 DBI                    1.1.3     2022-06-18 [1] CRAN (R 4.3.0)
 dbplyr                 2.3.2     2023-03-21 [1] CRAN (R 4.3.0)
 DelayedArray           0.26.1    2023-05-01 [1] Bioconductor
 derfinder              1.34.0    2023-04-25 [1] Bioconductor
 derfinderHelper        1.34.0    2023-04-25 [1] Bioconductor
 devtools             * 2.4.5     2022-10-11 [1] CRAN (R 4.3.0)
 digest                 0.6.31    2022-12-11 [1] CRAN (R 4.3.0)
 doRNG                  1.8.6     2023-01-16 [1] CRAN (R 4.3.0)
 downloader             0.4       2015-07-09 [1] CRAN (R 4.3.0)
 dplyr                  1.1.2     2023-04-20 [1] CRAN (R 4.3.0)
 ellipsis               0.3.2     2021-04-29 [1] CRAN (R 4.3.0)
 evaluate               0.21      2023-05-05 [1] CRAN (R 4.3.0)
 fansi                  1.0.4     2023-01-22 [1] CRAN (R 4.3.0)
 fastmap                1.1.1     2023-02-24 [1] CRAN (R 4.3.0)
 filelock               1.0.2     2018-10-05 [1] CRAN (R 4.3.0)
 foreach                1.5.2     2022-02-02 [1] CRAN (R 4.3.0)
 foreign                0.8-84    2022-12-06 [1] CRAN (R 4.3.0)
 Formula                1.2-5     2023-02-24 [1] CRAN (R 4.3.0)
 fs                     1.6.2     2023-04-25 [1] CRAN (R 4.3.0)
 generics               0.1.3     2022-07-05 [1] CRAN (R 4.3.0)
 GenomeInfoDb           1.36.0    2023-04-25 [1] Bioconductor
 GenomeInfoDbData       1.2.10    2023-05-06 [1] Bioconductor
 GenomicAlignments      1.36.0    2023-04-25 [1] Bioconductor
 GenomicFeatures        1.52.0    2023-04-25 [1] Bioconductor
 GenomicFiles           1.36.0    2023-04-25 [1] Bioconductor
 GenomicRanges          1.52.0    2023-04-25 [1] Bioconductor
 GEOquery               2.68.0    2023-04-25 [1] Bioconductor
 ggplot2                3.4.2     2023-04-03 [1] CRAN (R 4.3.0)
 glue                   1.6.2     2022-02-24 [1] CRAN (R 4.3.0)
 gridExtra              2.3       2017-09-09 [1] CRAN (R 4.3.0)
 gtable                 0.3.3     2023-03-21 [1] CRAN (R 4.3.0)
 Hmisc                  5.0-1     2023-03-08 [1] CRAN (R 4.3.0)
 hms                    1.1.3     2023-03-21 [1] CRAN (R 4.3.0)
 htmlTable              2.4.1     2022-07-07 [1] CRAN (R 4.3.0)
 htmltools              0.5.5     2023-03-23 [1] CRAN (R 4.3.0)
 htmlwidgets            1.6.2     2023-03-17 [1] CRAN (R 4.3.0)
 httpuv                 1.6.9     2023-02-14 [1] CRAN (R 4.3.0)
 httr                   1.4.5     2023-02-24 [1] CRAN (R 4.3.0)
 IRanges                2.34.0    2023-04-25 [1] Bioconductor
 iterators              1.0.14    2022-02-05 [1] CRAN (R 4.3.0)
 jsonlite               1.8.4     2022-12-06 [1] CRAN (R 4.3.0)
 KEGGREST               1.40.0    2023-04-25 [1] Bioconductor
 knitr                  1.42      2023-01-25 [1] CRAN (R 4.3.0)
 later                  1.3.1     2023-05-02 [1] CRAN (R 4.3.0)
 lattice                0.21-8    2023-04-05 [1] CRAN (R 4.3.0)
 lifecycle              1.0.3     2022-10-07 [1] CRAN (R 4.3.0)
 limma                  3.56.0    2023-04-25 [1] Bioconductor
 locfit                 1.5-9.7   2023-01-02 [1] CRAN (R 4.3.0)
 lubridate              1.9.2     2023-02-10 [1] CRAN (R 4.3.0)
 magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.3.0)
 Matrix                 1.5-4     2023-04-04 [1] CRAN (R 4.3.0)
 MatrixGenerics         1.12.0    2023-04-25 [1] Bioconductor
 matrixStats            0.63.0    2022-11-18 [1] CRAN (R 4.3.0)
 memoise                2.0.1     2021-11-26 [1] CRAN (R 4.3.0)
 mime                   0.12      2021-09-28 [1] CRAN (R 4.3.0)
 miniUI                 0.1.1.1   2018-05-18 [1] CRAN (R 4.3.0)
 munsell                0.5.0     2018-06-12 [1] CRAN (R 4.3.0)
 nnet                   7.3-19    2023-05-03 [1] CRAN (R 4.3.0)
 pillar                 1.9.0     2023-03-22 [1] CRAN (R 4.3.0)
 pkgbuild               1.4.0     2022-11-27 [1] CRAN (R 4.3.0)
 pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.3.0)
 pkgload                1.3.2     2022-11-16 [1] CRAN (R 4.3.0)
 plyr                   1.8.8     2022-11-11 [1] CRAN (R 4.3.0)
 png                    0.1-8     2022-11-29 [1] CRAN (R 4.3.0)
 prettyunits            1.1.1     2020-01-24 [1] CRAN (R 4.3.0)
 processx               3.8.1     2023-04-18 [1] CRAN (R 4.3.0)
 profvis                0.3.8     2023-05-02 [1] CRAN (R 4.3.0)
 progress               1.2.2     2019-05-16 [1] CRAN (R 4.3.0)
 promises               1.2.0.1   2021-02-11 [1] CRAN (R 4.3.0)
 prompt                 1.0.1     2023-05-06 [1] Github (gaborcsardi/prompt@7ef0f2e)
 ps                     1.7.5     2023-04-18 [1] CRAN (R 4.3.0)
 purrr                  1.0.1     2023-01-10 [1] CRAN (R 4.3.0)
 qvalue                 2.32.0    2023-04-25 [1] Bioconductor
 R.cache                0.16.0    2022-07-21 [1] CRAN (R 4.3.0)
 R.methodsS3            1.8.2     2022-06-13 [1] CRAN (R 4.3.0)
 R.oo                   1.25.0    2022-06-12 [1] CRAN (R 4.3.0)
 R.utils                2.12.2    2022-11-11 [1] CRAN (R 4.3.0)
 R6                     2.5.1     2021-08-19 [1] CRAN (R 4.3.0)
 rappdirs               0.3.3     2021-01-31 [1] CRAN (R 4.3.0)
 Rcpp                   1.0.10    2023-01-22 [1] CRAN (R 4.3.0)
 RCurl                  1.98-1.12 2023-03-27 [1] CRAN (R 4.3.0)
 readr                  2.1.4     2023-02-10 [1] CRAN (R 4.3.0)
 recount                1.26.0    2023-04-25 [1] Bioconductor
 recount3               1.9.1     2023-01-11 [1] Bioconductor
 remotes                2.4.2     2021-11-30 [1] CRAN (R 4.3.0)
 rentrez                1.2.3     2020-11-10 [1] CRAN (R 4.3.0)
 reshape2               1.4.4     2020-04-09 [1] CRAN (R 4.3.0)
 restfulr               0.0.15    2022-06-16 [1] CRAN (R 4.3.0)
 rjson                  0.2.21    2022-01-09 [1] CRAN (R 4.3.0)
 rlang                  1.1.1     2023-04-28 [1] CRAN (R 4.3.0)
 rmarkdown              2.21      2023-03-26 [1] CRAN (R 4.3.0)
 rngtools               1.5.2     2021-09-20 [1] CRAN (R 4.3.0)
 rpart                  4.1.19    2022-10-21 [1] CRAN (R 4.3.0)
 Rsamtools              2.16.0    2023-04-25 [1] Bioconductor
 RSQLite                2.3.1     2023-04-03 [1] CRAN (R 4.3.0)
 rsthemes               0.4.0     2023-05-06 [1] Github (gadenbuie/rsthemes@34a55a4)
 rstudioapi             0.14      2022-08-22 [1] CRAN (R 4.3.0)
 rtracklayer            1.60.0    2023-04-25 [1] Bioconductor
 S4Arrays               1.0.1     2023-05-01 [1] Bioconductor
 S4Vectors              0.38.1    2023-05-02 [1] Bioconductor
 scales                 1.2.1     2022-08-20 [1] CRAN (R 4.3.0)
 sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.3.0)
 shiny                  1.7.4     2022-12-15 [1] CRAN (R 4.3.0)
 stringi                1.7.12    2023-01-11 [1] CRAN (R 4.3.0)
 stringr                1.5.0     2022-12-02 [1] CRAN (R 4.3.0)
 styler                 1.9.1     2023-03-04 [1] CRAN (R 4.3.0)
 SummarizedExperiment   1.30.1    2023-05-01 [1] Bioconductor
 suncalc                0.5.1     2022-09-29 [1] CRAN (R 4.3.0)
 testthat             * 3.1.8     2023-05-04 [1] CRAN (R 4.3.0)
 tibble                 3.2.1     2023-03-20 [1] CRAN (R 4.3.0)
 tidyr                  1.3.0     2023-01-24 [1] CRAN (R 4.3.0)
 tidyselect             1.2.0     2022-10-10 [1] CRAN (R 4.3.0)
 timechange             0.2.0     2023-01-11 [1] CRAN (R 4.3.0)
 tzdb                   0.3.0     2022-03-28 [1] CRAN (R 4.3.0)
 urlchecker             1.0.1     2021-11-30 [1] CRAN (R 4.3.0)
 usethis              * 2.1.6     2022-05-25 [1] CRAN (R 4.3.0)
 utf8                   1.2.3     2023-01-31 [1] CRAN (R 4.3.0)
 VariantAnnotation      1.46.0    2023-04-25 [1] Bioconductor
 vctrs                  0.6.2     2023-04-19 [1] CRAN (R 4.3.0)
 withr                  2.5.0     2022-03-03 [1] CRAN (R 4.3.0)
 xfun                   0.39      2023-04-20 [1] CRAN (R 4.3.0)
 XML                    3.99-0.14 2023-03-19 [1] CRAN (R 4.3.0)
 xml2                   1.3.4     2023-04-27 [1] CRAN (R 4.3.0)
 xtable                 1.8-4     2019-04-21 [1] CRAN (R 4.3.0)
 XVector                0.40.0    2023-04-25 [1] Bioconductor
 yaml                   2.3.7     2023-01-23 [1] CRAN (R 4.3.0)
 zlibbioc               1.46.0    2023-04-25 [1] Bioconductor

 [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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devel > rse
class: RangedSummarizedExperiment 
dim: 64837 1048 
metadata(8): time_created recount3_version ... annotation recount3_url
assays(3): raw_counts counts TPM
rownames(64837): ENSG00000278704.1 ENSG00000277400.1 ... ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y
rowData names(10): source type ... havana_gene tag
colnames(1048): GTEX-R55C-0005-SM-3GAE9.1 GTEX-QMR6-0005-SM-32PKY.1 ... GTEX-1NSGN-0005-SM-DKPPX.1
  GTEX-1QP29-0005-SM-DLZQX.1
colData names(198): rail_id external_id ... recount_seq_qc.errq BigWigURL

@lcolladotor lcolladotor added the bug Something isn't working label Nov 30, 2023
@lcolladotor lcolladotor added this to the bioc v3.20 milestone Nov 30, 2023
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recount3 plans
Status: Todo
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bioc v3.20
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@lcolladotor @SoniaRuiz