The nullrangesData package provides datasets for the nullranges package vignette, in particular example datasets for exclusion regions, DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions.

library(nullrangesData)
## Loading required package: ExperimentHub
## Loading required package: BiocGenerics
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
##     as.data.frame, basename, cbind, colnames, dirname, do.call,
##     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
##     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
##     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
##     tapply, union, unique, unsplit, which.max, which.min
## Loading required package: AnnotationHub
## Loading required package: BiocFileCache
## Loading required package: dbplyr
## Loading required package: GenomicRanges
## Loading required package: stats4
## Loading required package: S4Vectors
## 
## Attaching package: 'S4Vectors'
## The following objects are masked from 'package:base':
## 
##     I, expand.grid, unname
## Loading required package: IRanges
## Loading required package: GenomeInfoDb
## Loading required package: InteractionSet
## Loading required package: SummarizedExperiment
## Loading required package: MatrixGenerics
## Loading required package: matrixStats
## 
## Attaching package: 'MatrixGenerics'
## The following objects are masked from 'package:matrixStats':
## 
##     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
##     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
##     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
##     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
##     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
##     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
##     colWeightedMeans, colWeightedMedians, colWeightedSds,
##     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
##     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
##     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
##     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
##     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
##     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
##     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
##     rowWeightedSds, rowWeightedVars
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## 
## Attaching package: 'Biobase'
## The following object is masked from 'package:MatrixGenerics':
## 
##     rowMedians
## The following objects are masked from 'package:matrixStats':
## 
##     anyMissing, rowMedians
## The following object is masked from 'package:ExperimentHub':
## 
##     cache
## The following object is masked from 'package:AnnotationHub':
## 
##     cache
## snapshotDate(): 2021-10-18
suppressPackageStartupMessages(library(GenomicRanges))
suppressPackageStartupMessages(library(InteractionSet))

A549 DHS peaks (see ?DHSA549Hg38 for details).

dhs <- DHSA549Hg38()
## see ?nullrangesData and browseVignettes('nullrangesData') for documentation
## loading from cache
dhs
## GRanges object with 177085 ranges and 6 metadata columns:
##            seqnames            ranges strand |        name     score
##               <Rle>         <IRanges>  <Rle> | <character> <numeric>
##        [1]     chr1       10181-10330      * |        <NA>         0
##        [2]     chr1     267990-268139      * |        <NA>         0
##        [3]     chr1     629126-629275      * |        <NA>         0
##        [4]     chr1     629306-629455      * |        <NA>         0
##        [5]     chr1     629901-630170      * |        <NA>         0
##        ...      ...               ...    ... .         ...       ...
##   [177081]     chrY 56873654-56873803      * |        <NA>         0
##   [177082]     chrY 56874534-56874683      * |        <NA>         0
##   [177083]     chrY 56883699-56883848      * |        <NA>         0
##   [177084]     chrY 56885199-56885348      * |        <NA>         0
##   [177085]     chrY 56886199-56886348      * |        <NA>         0
##            signalValue    pValue    qValue      peak
##              <numeric> <numeric> <numeric> <numeric>
##        [1]           6        -1        -1        -1
##        [2]          12        -1        -1        -1
##        [3]         378        -1        -1        -1
##        [4]         196        -1        -1        -1
##        [5]         212        -1        -1        -1
##        ...         ...       ...       ...       ...
##   [177081]          12        -1        -1        -1
##   [177082]          17        -1        -1        -1
##   [177083]          19        -1        -1        -1
##   [177084]          18        -1        -1        -1
##   [177085]          14        -1        -1        -1
##   -------
##   seqinfo: 24 sequences from hg38 genome

CTCF binding sites, 10kb bins with CTCF and DHS peaks, and CTCF-bound genomics interactions. See corresponding man pages for details.

bins <- hg19_10kb_bins()
## see ?nullrangesData and browseVignettes('nullrangesData') for documentation
## loading from cache
binPairs <- hg19_10kb_ctcfBoundBinPairs()
## see ?nullrangesData and browseVignettes('nullrangesData') for documentation
## loading from cache
bins
## GRanges object with 303641 ranges and 5 metadata columns:
##            seqnames              ranges strand | n_ctcf_sites ctcfSignal
##               <Rle>           <IRanges>  <Rle> |    <numeric>  <numeric>
##        [1]     chr1             1-10000      * |            0          0
##        [2]     chr1         10001-20000      * |            0          0
##        [3]     chr1         20001-30000      * |            0          0
##        [4]     chr1         30001-40000      * |            0          0
##        [5]     chr1         40001-50000      * |            0          0
##        ...      ...                 ...    ... .          ...        ...
##   [303637]     chrX 155230001-155240000      * |            0    0.00000
##   [303638]     chrX 155240001-155250000      * |            0    0.00000
##   [303639]     chrX 155250001-155260000      * |            1    4.09522
##   [303640]     chrX 155260001-155270000      * |            0    0.00000
##   [303641]     chrX 155270001-155270560      * |            0    0.00000
##            n_dnase_sites dnaseSignal    looped
##                 <factor>   <numeric> <logical>
##        [1]             0     0.00000     FALSE
##        [2]             0     5.03572     FALSE
##        [3]             0     0.00000     FALSE
##        [4]             0     0.00000     FALSE
##        [5]             0     0.00000     FALSE
##        ...           ...         ...       ...
##   [303637]             0     8.42068     FALSE
##   [303638]             0     4.08961     FALSE
##   [303639]             0     6.00443     FALSE
##   [303640]             0     8.07179     FALSE
##   [303641]             0     0.00000     FALSE
##   -------
##   seqinfo: 23 sequences from hg19 genome
binPairs
## StrictGInteractions object with 198120 interactions and 5 metadata columns:
##            seqnames1             ranges1     seqnames2             ranges2 |
##                <Rle>           <IRanges>         <Rle>           <IRanges> |
##        [1]      chr1       230001-240000 ---      chr1       520001-530000 |
##        [2]      chr1       230001-240000 ---      chr1       710001-720000 |
##        [3]      chr1       230001-240000 ---      chr1       800001-810000 |
##        [4]      chr1       230001-240000 ---      chr1       840001-850000 |
##        [5]      chr1       230001-240000 ---      chr1       870001-880000 |
##        ...       ...                 ... ...       ...                 ... .
##   [198116]      chrX 154310001-154320000 ---      chrX 154370001-154380000 |
##   [198117]      chrX 154310001-154320000 ---      chrX 155250001-155260000 |
##   [198118]      chrX 154320001-154330000 ---      chrX 154370001-154380000 |
##   [198119]      chrX 154320001-154330000 ---      chrX 155250001-155260000 |
##   [198120]      chrX 154370001-154380000 ---      chrX 155250001-155260000 |
##               looped ctcfSignal  n_sites  distance convergent
##            <logical>  <numeric> <factor> <integer>  <logical>
##        [1]     FALSE    5.18038        2    290000      FALSE
##        [2]     FALSE    5.46775        2    480000       TRUE
##        [3]     FALSE    7.30942        2    570000      FALSE
##        [4]     FALSE    7.34338        2    610000      FALSE
##        [5]     FALSE    6.31338        3    640000       TRUE
##        ...       ...        ...      ...       ...        ...
##   [198116]     FALSE    6.79246        2     60000      FALSE
##   [198117]     FALSE    6.12447        3    940000       TRUE
##   [198118]     FALSE    7.40868        2     50000       TRUE
##   [198119]     FALSE    7.00936        3    930000      FALSE
##   [198120]     FALSE    6.73402        3    880000       TRUE
##   -------
##   regions: 20612 ranges and 5 metadata columns
##   seqinfo: 23 sequences from hg19 genome

Session information

sessionInfo()
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
## 
## 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       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] nullrangesData_1.0.0        InteractionSet_1.22.0      
##  [3] SummarizedExperiment_1.24.0 Biobase_2.54.0             
##  [5] MatrixGenerics_1.6.0        matrixStats_0.61.0         
##  [7] GenomicRanges_1.46.0        GenomeInfoDb_1.30.0        
##  [9] IRanges_2.28.0              S4Vectors_0.32.0           
## [11] ExperimentHub_2.2.0         AnnotationHub_3.2.0        
## [13] BiocFileCache_2.2.0         dbplyr_2.1.1               
## [15] BiocGenerics_0.40.0        
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7                    lattice_0.20-45              
##  [3] png_0.1-7                     Biostrings_2.62.0            
##  [5] assertthat_0.2.1              digest_0.6.28                
##  [7] utf8_1.2.2                    mime_0.12                    
##  [9] R6_2.5.1                      RSQLite_2.2.8                
## [11] evaluate_0.14                 httr_1.4.2                   
## [13] pillar_1.6.4                  zlibbioc_1.40.0              
## [15] rlang_0.4.12                  curl_4.3.2                   
## [17] jquerylib_0.1.4               blob_1.2.2                   
## [19] Matrix_1.3-4                  rmarkdown_2.11               
## [21] stringr_1.4.0                 RCurl_1.98-1.5               
## [23] bit_4.0.4                     DelayedArray_0.20.0          
## [25] shiny_1.7.1                   compiler_4.1.1               
## [27] httpuv_1.6.3                  xfun_0.27                    
## [29] pkgconfig_2.0.3               htmltools_0.5.2              
## [31] tidyselect_1.1.1              KEGGREST_1.34.0              
## [33] tibble_3.1.5                  GenomeInfoDbData_1.2.7       
## [35] interactiveDisplayBase_1.32.0 fansi_0.5.0                  
## [37] withr_2.4.2                   crayon_1.4.1                 
## [39] dplyr_1.0.7                   later_1.3.0                  
## [41] bitops_1.0-7                  rappdirs_0.3.3               
## [43] grid_4.1.1                    jsonlite_1.7.2               
## [45] xtable_1.8-4                  lifecycle_1.0.1              
## [47] DBI_1.1.1                     magrittr_2.0.1               
## [49] stringi_1.7.5                 cachem_1.0.6                 
## [51] XVector_0.34.0                promises_1.2.0.1             
## [53] bslib_0.3.1                   ellipsis_0.3.2               
## [55] filelock_1.0.2                generics_0.1.1               
## [57] vctrs_0.3.8                   tools_4.1.1                  
## [59] bit64_4.0.5                   glue_1.4.2                   
## [61] purrr_0.3.4                   BiocVersion_3.14.0           
## [63] fastmap_1.1.0                 yaml_2.2.1                   
## [65] AnnotationDbi_1.56.1          BiocManager_1.30.16          
## [67] memoise_2.0.0                 knitr_1.36                   
## [69] sass_0.4.0