The nullrangesData package provides datasets for the nullranges package vignette, in particular example datasets for exclusion regions, DNase hypersensitivity sites (DHS), Single Cell Multiome ATAC and Gene Expression assay, CTCF binding sites, and CTCF genomic interactions.
library(nullrangesData)## Loading required package: ExperimentHub## Loading required package: BiocGenerics##
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## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
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## cachesuppressPackageStartupMessages(library(GenomicRanges))
suppressPackageStartupMessages(library(InteractionSet))A549 DHS peaks (see ?DHSA549Hg38 for details).
dhs <- DHSA549Hg38()## see ?nullrangesData and browseVignettes('nullrangesData') for documentation## loading from cachedhs## 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 genomeChromium Single Cell Multiome ATAC + Gene Expression assay. See corresponding man pages for details..
data("sc_rna")
data("sc_promoter")
sc_rna## GRanges object with 28225 ranges and 2 metadata columns:
## seqnames ranges strand | gene
## <Rle> <IRanges> <Rle> | <character>
## [1] chr1 120931-133723 * | AL627309.1
## [2] chr1 140338-140339 * | AL627309.2
## [3] chr1 149706-173862 * | AL627309.5
## [4] chr1 160445-160446 * | AL627309.4
## [5] chr1 266854-266855 * | AP006222.2
## ... ... ... ... . ...
## [28221] chr22 50597151-50597152 * | U62317.3
## [28222] chr22 50600792-50600793 * | MAPK8IP2
## [28223] chr22 50628151-50628173 * | ARSA
## [28224] chr22 50674641-50729572 * | SHANK3
## [28225] chr22 50783620-50783663 * | RABL2B
## counts1
## <NumericList>
## [1] -0.227594, 0.249144, 0.419668,...
## [2] -0.267261,-0.267261,-0.267261,...
## [3] -0.39115,-0.10318, 1.02400,...
## [4] 0.1516318,-0.0605821, 1.9885284,...
## [5] -0.267261,-0.267261,-0.267261,...
## ... ...
## [28221] -0.267261,-0.267261,-0.267261,...
## [28222] 0.701249,-0.546908,-0.546908,...
## [28223] -0.509022, 0.201242, 1.618880,...
## [28224] -0.267261,-0.267261,-0.267261,...
## [28225] 0.9252646,-0.0774203,-0.2877604,...
## -------
## seqinfo: 22 sequences from an unspecified genome; no seqlengthssc_promoter## GRanges object with 15561 ranges and 2 metadata columns:
## seqnames ranges strand | peak
## <Rle> <IRanges> <Rle> | <character>
## [1] chr1 777634-779926 * | chr1:777634-779926
## [2] chr1 816881-817647 * | chr1:816881-817647
## [3] chr1 826612-827979 * | chr1:826612-827979
## [4] chr1 869449-870383 * | chr1:869449-870383
## [5] chr1 903617-907386 * | chr1:903617-907386
## ... ... ... ... . ...
## [15557] chr22 50580287-50583942 * | chr22:50580287-50583..
## [15558] chr22 50599877-50602115 * | chr22:50599877-50602..
## [15559] chr22 50625295-50629340 * | chr22:50625295-50629..
## [15560] chr22 50671698-50675683 * | chr22:50671698-50675..
## [15561] chr22 50783058-50784322 * | chr22:50783058-50784..
## counts2
## <NumericList>
## [1] 1.143068,0.383233,0.342632,...
## [2] -0.618560,-0.415192, 1.277454,...
## [3] -1.162635,-0.571467, 1.045412,...
## [4] 0.923427, 0.797197,-1.394984,...
## [5] 0.337377,-0.727911, 1.501327,...
## ... ...
## [15557] 1.068434, 0.345541,-0.229966,...
## [15558] 0.500332, 0.458059,-1.085105,...
## [15559] 0.2946085,-0.0665503,-0.6663091,...
## [15560] 0.705884,-0.272306,-0.326069,...
## [15561] 0.149851, 0.460193,-0.192810,...
## -------
## seqinfo: 22 sequences from an unspecified genome; no seqlengthsCTCF 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 cachebinPairs <- hg19_10kb_ctcfBoundBinPairs()## see ?nullrangesData and browseVignettes('nullrangesData') for documentation
## loading from cachebins## 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 genomebinPairs## 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 genomesessionInfo()## R version 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
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## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
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## time zone: America/New_York
## tzcode source: system (glibc)
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## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
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## other attached packages:
## [1] nullrangesData_1.10.0 InteractionSet_1.32.0
## [3] SummarizedExperiment_1.34.0 Biobase_2.64.0
## [5] MatrixGenerics_1.16.0 matrixStats_1.3.0
## [7] GenomicRanges_1.56.0 GenomeInfoDb_1.40.0
## [9] IRanges_2.38.0 S4Vectors_0.42.0
## [11] ExperimentHub_2.12.0 AnnotationHub_3.12.0
## [13] BiocFileCache_2.12.0 dbplyr_2.5.0
## [15] BiocGenerics_0.50.0
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## loaded via a namespace (and not attached):
## [1] KEGGREST_1.44.0 xfun_0.43 bslib_0.7.0
## [4] lattice_0.22-6 vctrs_0.6.5 tools_4.4.0
## [7] generics_0.1.3 curl_5.2.1 tibble_3.2.1
## [10] fansi_1.0.6 AnnotationDbi_1.66.0 RSQLite_2.3.6
## [13] blob_1.2.4 pkgconfig_2.0.3 Matrix_1.7-0
## [16] lifecycle_1.0.4 GenomeInfoDbData_1.2.12 compiler_4.4.0
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## [31] digest_0.6.35 purrr_1.0.2 dplyr_1.1.4
## [34] BiocVersion_3.19.1 grid_4.4.0 fastmap_1.1.1
## [37] SparseArray_1.4.0 cli_3.6.2 magrittr_2.0.3
## [40] S4Arrays_1.4.0 utf8_1.2.4 withr_3.0.0
## [43] filelock_1.0.3 UCSC.utils_1.0.0 rappdirs_0.3.3
## [46] bit64_4.0.5 rmarkdown_2.26 XVector_0.44.0
## [49] httr_1.4.7 bit_4.0.5 png_0.1-8
## [52] memoise_2.0.1 evaluate_0.23 knitr_1.46
## [55] rlang_1.1.3 Rcpp_1.0.12 glue_1.7.0
## [58] DBI_1.2.2 BiocManager_1.30.22 jsonlite_1.8.8
## [61] R6_2.5.1 zlibbioc_1.50.0