The bodymapRat package contains gene expression data on
652 RNA-Seq samples from a comprehensive rat transcriptomic BodyMap
study. These samples include the sequence identifier information
provided in the header of the FASTQ files which can be used as a
surrogate for batch. These samples have not been normalized or
pre-processed.
The data are provided in a SummarizedExperiment. The
phenotypic information can be extracted using the colData()
function and a description of the phenotypic data is listed in the table
below:
| Title | Description |
|---|---|
| sraExperiment | SRA Experiment ID |
| title | Title of sample provided by the authors |
| geoAccession | GEO Accession ID |
| BioSample | BioSample ID |
| avgLength | Average read length |
| instrument | Machine identifier (from FASTQ header) |
| runID | Run ID (from FASTQ header) |
| fcID | Flow cell ID (from FASTQ header) |
| fcLane | Flow cell lane (from FASTQ header) |
| tile | Tile (from FASTQ header) |
| xtile | xtile (from FASTQ header) |
| ytile | ytile (from FASTQ header) |
| organ | Body organ |
| sex | Gender |
| stage | Stage |
| techRep | Technical replicate number |
| colOrgan | Column of colors to help with plotting |
| rnaRIN | RIN number |
| barcode | barcode number |
The data can be accessed as follows:
We use the bodymapRat() function to download the
relevant files from Bioconductor’s ExperimentHub
web resource. Running this function will download a
SummarizedExperiment object, which contains read counts, as
well as the metadata on the rows (genes) and columns (cells).
## [1] 32637 652## SRR1169893 SRR1169894 SRR1169895 SRR1169896 SRR1169897
## ENSRNOG00000000001 1 0 0 1 4
## ENSRNOG00000000007 1 1 0 3 0
## ENSRNOG00000000008 7 4 2 3 7
## ENSRNOG00000000009 0 0 0 0 1
## ENSRNOG00000000010 0 1 0 0 0## DataFrame with 6 rows and 22 columns
## sraExperiment sraRun title geoAccession sraSample
## <character> <character> <character> <factor> <factor>
## SRR1169893 SRX471368 SRR1169893 Adr_F_002_1 GSM1328469 SRS558114
## SRR1169894 SRX471368 SRR1169894 Adr_F_002_1 GSM1328469 SRS558114
## SRR1169895 SRX471369 SRR1169895 Adr_F_002_2 GSM1328470 SRS558115
## SRR1169896 SRX471369 SRR1169896 Adr_F_002_2 GSM1328470 SRS558115
## SRR1169897 SRX471370 SRR1169897 Adr_F_002_3 GSM1328471 SRS558116
## SRR1169898 SRX471370 SRR1169898 Adr_F_002_3 GSM1328471 SRS558116
## BioSample avgLength organ sex stage techRep
## <factor> <integer> <character> <character> <numeric> <integer>
## SRR1169893 SAMN02642886 50 Adrenal F 2 1
## SRR1169894 SAMN02642886 50 Adrenal F 2 2
## SRR1169895 SAMN02642867 50 Adrenal F 2 1
## SRR1169896 SAMN02642867 50 Adrenal F 2 2
## SRR1169897 SAMN02642894 50 Adrenal F 2 1
## SRR1169898 SAMN02642894 50 Adrenal F 2 2
## colOrgan mix rnaRIN barcode instrument
## <character> <character> <character> <character> <character>
## SRR1169893 brown M1 9.3 11 HWI-ST845
## SRR1169894 brown M1 9.3 11 HWI-ST845
## SRR1169895 brown M1 9.1 5 HWI-ST845
## SRR1169896 brown M1 9.1 5 HWI-ST845
## SRR1169897 brown M1 9.5 3 HWI-ST1131
## SRR1169898 brown M1 9.5 3 HWI-ST1195
## runID fcID fcLane tile xtile
## <character> <character> <character> <character> <character>
## SRR1169893 120326 D0VTJACXX 2 1101 1506
## SRR1169894 120525 D10G7ACXX 2 1101 1394
## SRR1169895 120326 D0VTJACXX 5 1101 1170
## SRR1169896 120525 D10G7ACXX 5 1101 1650
## SRR1169897 120424 C0P4UACXX 4 1101 1675
## SRR1169898 120525 C0TDUACXX 4 1101 1138
## ytile
## <character>
## SRR1169893 2000
## SRR1169894 2133
## SRR1169895 2029
## SRR1169896 2126
## SRR1169897 2216
## SRR1169898 2067The data in this package are used as an example data set in the qsmooth
Bioconductor package.
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] bodymapRat_1.29.0 ExperimentHub_3.3.2
## [3] AnnotationHub_4.3.2 BiocFileCache_3.3.0
## [5] dbplyr_2.6.0 SummarizedExperiment_1.43.0
## [7] Biobase_2.73.2 GenomicRanges_1.65.4
## [9] Seqinfo_1.3.2 IRanges_2.47.5
## [11] S4Vectors_0.51.10 BiocGenerics_0.59.12
## [13] generics_0.1.4 MatrixGenerics_1.25.0
## [15] matrixStats_1.5.0 knitr_1.52
## [17] BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.53.6 xfun_0.61 bslib_0.12.0
## [4] httr2_1.3.0 lattice_0.23-1 vctrs_0.7.3
## [7] tools_4.6.1 curl_8.0.0 tibble_3.3.1
## [10] AnnotationDbi_1.75.2 RSQLite_3.53.3 blob_1.3.0
## [13] pkgconfig_2.0.3 BiocBaseUtils_1.15.1 Matrix_1.7-6
## [16] lifecycle_1.0.5 compiler_4.6.1 Biostrings_2.81.9
## [19] htmltools_0.5.9 sys_3.4.3 buildtools_1.0.0
## [22] sass_0.4.10 yaml_2.3.12 pillar_1.11.1
## [25] crayon_1.5.3 jquerylib_0.1.4 DelayedArray_0.39.8
## [28] cachem_1.1.0 abind_1.4-8 tidyselect_1.2.1
## [31] digest_0.6.39 purrr_1.2.2 dplyr_1.2.1
## [34] BiocVersion_3.24.0 maketools_1.3.2 fastmap_1.2.0
## [37] grid_4.6.1 cli_3.6.6 SparseArray_1.13.4
## [40] magrittr_2.0.5 S4Arrays_1.13.2 withr_3.0.3
## [43] filelock_1.0.3 rappdirs_0.3.4 bit64_4.8.6
## [46] rmarkdown_2.32 XVector_0.53.0 httr_1.4.9
## [49] bit_4.6.0 otel_0.2.0 png_0.1-9
## [52] memoise_2.0.1 evaluate_1.0.5 rlang_1.3.0
## [55] glue_1.8.1 DBI_1.3.0 BiocManager_1.30.27
## [58] jsonlite_2.0.0 R6_2.6.1