loopcityData provides the experimental data used in
examples and vignettes for the loopcity package.
Two datasets ship directly with the package (accessible via
data()). Larger files — K562 Hi-C contact matrices and
ChIP-seq bigWig tracks — are hosted on ExperimentHub and downloaded to a
local cache on first use.
library(loopcityData)
#> Loading required package: ExperimentHub
#> Loading required package: BiocGenerics
#> Loading required package: generics
#>
#> Attaching package: 'generics'
#> The following objects are masked from 'package:base':
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#> as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#> setequal, union
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#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
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#> data
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#> rbind, Reduce, rownames, sapply, saveRDS, scale, sequence, table,
#> tapply, transform, unique, unsplit, which.max, which.min
#> Loading required package: AnnotationHub
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#> Loading required package: dbplyr
data(GM12878_10KbLoops)
GM12878_10KbLoops
#> Loading required namespace: InteractionSet
#> GInteractions object with 175 interactions and 9 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 |
#> <Rle> <IRanges> <Rle> <IRanges> |
#> [1] 22 33910000-33920000 --- 22 34510000-34520000 |
#> [2] 22 42360000-42370000 --- 22 42830000-42840000 |
#> [3] 22 32920000-32930000 --- 22 33390000-33400000 |
#> [4] 22 50320000-50330000 --- 22 50640000-50650000 |
#> [5] 22 50710000-50720000 --- 22 51050000-51060000 |
#> ... ... ... ... ... ... .
#> [171] 22 42090000-42100000 --- 22 42330000-42340000 |
#> [172] 22 30680000-30690000 --- 22 30750000-30760000 |
#> [173] 22 31020000-31030000 --- 22 31470000-31480000 |
#> [174] 22 25630000-25640000 --- 22 25730000-25740000 |
#> [175] 22 20760000-20770000 --- 22 20810000-20820000 |
#> color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <character> <numeric> <numeric> <numeric>
#> [1] 0,0,0 4.44026 0.995566 2.31370
#> [2] 0,0,0 3.22755 0.992109 2.50512
#> [3] 0,0,0 3.52515 0.996723 2.30686
#> [4] 0,0,0 7.38547 1.000000 4.94431
#> [5] 0,0,0 2.70953 0.982758 1.93644
#> ... ... ... ... ...
#> [171] 0,0,0 4.00052 0.998340 2.45203
#> [172] 0,0,0 2.12425 0.979126 1.64941
#> [173] 0,0,0 2.20127 0.980618 1.62340
#> [174] 0,0,0 2.70770 0.972048 1.79979
#> [175] 0,0,0 1.98188 0.958774 1.53469
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std
#> <numeric> <numeric> <numeric> <numeric>
#> [1] 2.36334 2.87352 3.31830 1.283566
#> [2] 1.23290 1.80059 5.81512 0.830535
#> [3] 1.45465 2.36218 4.42827 0.765224
#> [4] 1.73833 2.27940 4.55122 1.064696
#> [5] 1.30807 2.02448 4.84536 0.976256
#> ... ... ... ... ...
#> [171] 2.704920 3.89185 6.26677 1.235414
#> [172] 0.676159 1.01348 3.26864 0.292162
#> [173] 0.969484 1.13294 3.08203 0.542739
#> [174] 0.909894 1.41944 2.76884 0.451721
#> [175] 0.517707 0.86547 2.72882 0.248452
#> value
#> <numeric>
#> [1] 5.41905
#> [2] 6.91103
#> [3] 5.72130
#> [4] 6.09641
#> [5] 6.00809
#> ... ...
#> [171] 8.67115
#> [172] 3.86967
#> [173] 3.94380
#> [174] 3.57763
#> [175] 3.18901
#> -------
#> regions: 262 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
data(GM12878_10KbLoopsChr21)
GM12878_10KbLoopsChr21
#> GInteractions object with 141 interactions and 9 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 |
#> <Rle> <IRanges> <Rle> <IRanges> |
#> [1] 21 43880000-43890000 --- 21 43940000-43950000 |
#> [2] 21 26980000-26990000 --- 21 28090000-28100000 |
#> [3] 21 27260000-27270000 --- 21 27540000-27550000 |
#> [4] 21 46560000-46570000 --- 21 47240000-47250000 |
#> [5] 21 34200000-34210000 --- 21 34490000-34500000 |
#> ... ... ... ... ... ... .
#> [137] 21 46970000-46980000 --- 21 47230000-47240000 |
#> [138] 21 46210000-46220000 --- 21 46350000-46360000 |
#> [139] 21 45090000-45100000 --- 21 45130000-45140000 |
#> [140] 21 22530000-22540000 --- 21 24160000-24170000 |
#> [141] 21 41510000-41520000 --- 21 42440000-42450000 |
#> color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <character> <numeric> <numeric> <numeric>
#> [1] 0,0,0 2.65898 0.984944 1.99320
#> [2] 0,0,0 6.74894 1.000000 2.95694
#> [3] 0,0,0 3.62774 0.996851 2.31951
#> [4] 0,0,0 2.95391 0.986015 2.01561
#> [5] 0,0,0 3.10370 0.996050 1.85707
#> ... ... ... ... ...
#> [137] 0,0,0 4.93171 0.999582 2.96703
#> [138] 0,0,0 2.98592 0.975592 2.14933
#> [139] 0,0,0 1.84811 0.928549 1.44126
#> [140] 0,0,0 4.83892 0.999990 2.01727
#> [141] 0,0,0 2.73185 0.991331 1.59490
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std
#> <numeric> <numeric> <numeric> <numeric>
#> [1] 0.791644 1.24593 3.49271 0.383759
#> [2] 3.189283 3.46806 2.93180 1.461620
#> [3] 1.652818 2.41993 4.29223 0.721309
#> [4] 1.736935 2.23437 4.70771 1.059107
#> [5] 2.371813 3.64524 5.58966 0.944114
#> ... ... ... ... ...
#> [137] 3.004317 4.845334 7.52684 1.633452
#> [138] 0.815103 1.218015 2.98869 0.509255
#> [139] 0.557756 0.628889 2.14324 0.248812
#> [140] 8.577646 8.711745 6.64423 3.669979
#> [141] 2.105123 3.371496 4.93202 1.185569
#> value
#> <numeric>
#> [1] 4.19639
#> [2] 5.76672
#> [3] 5.76140
#> [4] 6.25165
#> [5] 7.69794
#> ... ...
#> [137] 10.19735
#> [138] 3.71322
#> [139] 2.63902
#> [140] 14.26881
#> [141] 6.80324
#> -------
#> regions: 209 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengthsThe K562 datasets from Bond et al. 2023 are retrieved via ExperimentHub. Files are downloaded once and cached locally by BiocFileCache.
hic_path <- K562_hic()
loops_path <- K562_loops()
ctcf_path <- K562_CTCF_bw()
h3k27ac_path <- K562_H3K27ac_bw()These paths can be passed directly to loopcity functions
and plotgardener visualization functions. See the plotgardener
integration vignette in the loopcity package for a
worked example.
| Object | Accession | Reference |
|---|---|---|
GM12878_10KbLoops /
GM12878_10KbLoopsChr21 |
GSE63525 | Rao et al. 2014 |
K562_hic / K562_loops |
GSE214123 | Bond et al. 2023 |
K562_CTCF_bw / K562_H3K27ac_bw |
GSE213908 | Bond et al. 2023 |
sessionInfo()
#> R version 4.6.0 (2026-04-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.4 LTS
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#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
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#> other attached packages:
#> [1] loopcityData_0.99.0 ExperimentHub_3.3.1 AnnotationHub_4.3.1
#> [4] BiocFileCache_3.3.0 dbplyr_2.5.2 BiocGenerics_0.59.7
#> [7] generics_0.1.4 BiocStyle_2.41.0
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#> loaded via a namespace (and not attached):
#> [1] KEGGREST_1.53.0 SummarizedExperiment_1.43.0
#> [3] xfun_0.58 bslib_0.11.0
#> [5] httr2_1.2.2 lattice_0.22-9
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#> [13] AnnotationDbi_1.75.0 RSQLite_3.53.1
#> [15] blob_1.3.0 pkgconfig_2.0.3
#> [17] Matrix_1.7-5 S4Vectors_0.51.3
#> [19] lifecycle_1.0.5 compiler_4.6.0
#> [21] Biostrings_2.81.3 Seqinfo_1.3.0
#> [23] InteractionSet_1.41.0 htmltools_0.5.9
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#> [41] fastmap_1.2.0 SparseArray_1.13.2
#> [43] cli_3.6.6 magrittr_2.0.5
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#> [63] DBI_1.3.0 BiocManager_1.30.27
#> [65] jsonlite_2.0.0 R6_2.6.1
#> [67] MatrixGenerics_1.25.0