library(dominatRData)This package provides supplemental datasets and files for use with dominatR. For more information on how to use these data, please refer to the dominatR vignette.
The data is used for specific examples, such as three-way (triangle) visualization of RNA polymerase I, II, and III genomic occupancy dominance at enzyme-specific gene targets (Rajendra K C et al., 2024 Molecular Cell), or such as 19-way (circular) visualization of tissue-specific gene accessibility patterns at canonical RNA Pol III-transcribed genes (Simon Lizarazo et al., 2025 bioRxiv preprint).
To install this package, start R and enter:
library(BiocManager)
BiocManager::install('dominatRData')data("rnapol_counts")
head(rnapol_counts)
#> Chr Start Stop RNA_type pol1 pol2 pol3
#> 1 chr1 14612182 14612382 tRNA 27 14 19
#> 2 chr1 16520508 16520708 tRNA 6 26 993
#> 3 chr1 16534435 16534635 tRNA 32 52 71
#> 4 chr1 16535200 16535400 tRNA 11 62 4832
#> 5 chr1 16545862 16546062 tRNA 70 45 7078
#> 6 chr1 16547587 16547787 tRNA 35 23 1246
data("rnapol_score")
head(rnapol_score)
#> Chr Start Stop RNA_type pol1 pol2 pol3
#> 1 chr1 14612182 14612382 tRNA 2.29 0.19 0.16
#> 2 chr1 16520508 16520708 tRNA 0.03 0.00 118.76
#> 3 chr1 16534435 16534635 tRNA 1.13 0.19 0.00
#> 4 chr1 16535200 16535400 tRNA 0.08 0.26 319.13
#> 5 chr1 16545862 16546062 tRNA 2.60 0.19 319.13
#> 6 chr1 16547587 16547787 tRNA 0.40 0.15 72.30
data("atac_tissue_counts")
head(atac_tissue_counts)
#> core_type Chr Start End Gene
#> 1 Innactive chr21 17431546 17431647 U6_snRNA_URS0000705D4B&&100167
#> 2 75% Tissues chr21 17454788 17454859 tRNA-Gly-GCC-1-3&&100172
#> 3 Specific chr21 17484720 17484837 Metazoa_SRP_SRP_RNA_URS0000972307&&100175
#> 4 Innactive chr21 17502826 17502943 Metazoa_SRP_SRP_RNA_URS000099CB36&&100178
#> 5 Innactive chr21 17509814 17509961 Metazoa_SRP_SRP_RNA_URS0000995B6B&&100180
#> 6 Innactive chr21 20320659 20320806 Metazoa_SRP_SRP_RNA_URS0000915522&&100266
#> Index Type Heart Spleen Liver Colon Adrenal.Gland Lung Pancreas
#> 1 100167 u6 RNA 5 22 10 18 6 11 5
#> 2 100172 tRNA 662 1129 1378 1087 2330 2292 2804
#> 3 100175 SRP 8 45 48 21 14 26 12
#> 4 100178 SRP 7 21 14 19 3 15 9
#> 5 100180 SRP 8 32 15 18 7 21 12
#> 6 100266 SRP 6 27 12 15 4 13 6
#> Gallbladder Urinary.Tract Breast Fallopian.Tube Psoas.Muscle Vena.Cava
#> 1 14 17 17 19 6 17
#> 2 1628 1313 815 1623 2505 1535
#> 3 19 22 22 22 9 24
#> 4 24 19 13 21 9 16
#> 5 22 27 19 47 8 28
#> 6 14 29 26 16 8 20
#> Gastroesophageal.Sphincter Adipose.Tissue Sciatic.Nerve Ovary...Uterus
#> 1 15 12 18 15
#> 2 1277 1189 2070 2374
#> 3 20 18 26 22
#> 4 13 17 13 14
#> 5 23 20 19 16
#> 6 30 18 20 18
#> Stomach Brain
#> 1 15 35
#> 2 844 1114
#> 3 18 29
#> 4 20 31
#> 5 17 47
#> 6 17 38
data("atac_tissue_score")
head(atac_tissue_score)
#> core_type Chr Start End Gene
#> 1 Innactive chr21 17431546 17431647 U6_snRNA_URS0000705D4B&&100167
#> 2 75% Tissues chr21 17454788 17454859 tRNA-Gly-GCC-1-3&&100172
#> 3 Specific chr21 17484720 17484837 Metazoa_SRP_SRP_RNA_URS0000972307&&100175
#> 4 Innactive chr21 17502826 17502943 Metazoa_SRP_SRP_RNA_URS000099CB36&&100178
#> 5 Innactive chr21 17509814 17509961 Metazoa_SRP_SRP_RNA_URS0000995B6B&&100180
#> 6 Innactive chr21 20320659 20320806 Metazoa_SRP_SRP_RNA_URS0000915522&&100266
#> Index Type Heart Spleen Liver Colon Adrenal.Gland Lung Pancreas
#> 1 100167 u6 RNA 0 0 0 0 0 0 0
#> 2 100172 tRNA 1 1 1 1 1 1 1
#> 3 100175 SRP 0 1 0 0 0 0 0
#> 4 100178 SRP 0 0 0 0 0 0 0
#> 5 100180 SRP 0 0 0 0 0 0 0
#> 6 100266 SRP 0 0 0 0 0 0 0
#> Gallbladder Urinary.Tract Breast Fallopian.Tube Psoas.Muscle Vena.Cava
#> 1 0 0 0 0 0 0
#> 2 1 1 1 1 1 1
#> 3 0 0 0 0 0 0
#> 4 0 0 0 0 0 0
#> 5 0 0 0 0 0 0
#> 6 0 0 0 0 0 0
#> Gastroesophageal.Sphincter Adipose.Tissue Sciatic.Nerve Ovary...Uterus
#> 1 0 0 0 0
#> 2 1 1 1 1
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 0 0 0 0
#> 6 0 0 0 0
#> Stomach Brain
#> 1 0 0
#> 2 1 1
#> 3 0 0
#> 4 0 0
#> 5 0 0
#> 6 0 0sessionInfo()
#> R Under development (unstable) (2025-10-20 r88955)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.3 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB LC_COLLATE=C
#> [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: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] dominatRData_0.99.1 knitr_1.50
#>
#> loaded via a namespace (and not attached):
#> [1] digest_0.6.37 R6_2.6.1 fastmap_1.2.0 xfun_0.54
#> [5] cachem_1.1.0 htmltools_0.5.8.1 rmarkdown_2.30 lifecycle_1.0.4
#> [9] cli_3.6.5 sass_0.4.10 jquerylib_0.1.4 compiler_4.6.0
#> [13] tools_4.6.0 evaluate_1.0.5 bslib_0.9.0 yaml_2.3.10
#> [17] rlang_1.1.6 jsonlite_2.0.0