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)
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## Welcome to Bioconductor
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##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
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## snapshotDate(): 2022-04-19
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 4.2.0 RC (2022-04-21 r82226)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## locale:
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##  [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_1.3.0        InteractionSet_1.25.0      
##  [3] SummarizedExperiment_1.27.0 Biobase_2.57.0             
##  [5] MatrixGenerics_1.9.0        matrixStats_0.62.0         
##  [7] GenomicRanges_1.49.0        GenomeInfoDb_1.33.0        
##  [9] IRanges_2.31.0              S4Vectors_0.35.0           
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