recount::getTPM(rse) method

SoniaRuiz commented 1 year ago

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_rsemanual()', as it is reported on https://rdrr.io/bioc/recount/man/getTPM.html.

R Session Information

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

```R > 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

```R > 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 commented 1 year ago

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:

```R 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] 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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 ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── devel > ```

lcolladotor commented 1 year ago

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

LieberInstitute / recount3