HiCExperiment class#>
#> Extends: "Annotated"
#>
-#> Known Subclasses: "AggrHiCExperiment"
-
-hic <- contacts_yeast()
+#> Known Subclasses: "AggrHiCExperiment"
+hic <- contacts_yeast()
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache
-hic
+#> loading from cache
+hic
#> `HiCExperiment` object with 8,757,906 contacts over 763 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f0646279c31_7752"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc24e3419b1_7752"
#> focus: "whole genome"
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 16000
@@ -202,7 +200,7 @@ Import methods
The implemented import() methods allow one to import
Hi-C matrix files in R as HiCExperiment objects.
-
+
## Change <path/to/contact_matrix>.cool accordingly
hic <- import(
"<path/to/contact_matrix>.cool",
@@ -212,16 +210,15 @@ Import methodsTo give real-life examples, we use the HiContactsData
package to get access to a range of toy datasets available from the
ExperimentHub.
-
+
library(HiContactsData)
cool_file <- HiContactsData('yeast_wt', format = 'cool')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache
-
-import(cool_file, format = 'cool')
+#> loading from cache
+import(cool_file, format = 'cool')
#> `HiCExperiment` object with 8,757,906 contacts over 12,079 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f065f43dd61_7751"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc2169bc907_7751"
#> focus: "whole genome"
#> resolutions(1): 1000
#> active resolution: 1000
@@ -256,34 +253,31 @@ Supporting file classesFor each object, an optional pairsFile can be associated
and linked to the contact matrix file when imported as a
HiCExperiment object.
-
+
## --- CoolFile
pairs_file <- HiContactsData('yeast_wt', format = 'pairs.gz')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache
-
-coolf <- CoolFile(cool_file, pairsFile = pairs_file)
+#> loading from cache
+coolf <- CoolFile(cool_file, pairsFile = pairs_file)
coolf
#> CoolFile object
-#> .mcool file: /github/home/.cache/R/ExperimentHub/f065f43dd61_7751
+#> .mcool file: /github/home/.cache/R/ExperimentHub/dc2169bc907_7751
#> resolution: 1000
-#> pairs file: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
-#> metadata(0):
-
-import(coolf)
+#> pairs file: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
+#> metadata(0):
+import(coolf)
#> `HiCExperiment` object with 8,757,906 contacts over 12,079 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f065f43dd61_7751"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc2169bc907_7751"
#> focus: "whole genome"
#> resolutions(1): 1000
#> active resolution: 1000
#> interactions: 2945692
#> scores(2): count balanced
#> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
-#> pairsFile: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
-#> metadata(0):
-
-import(pairsFile(coolf), format = 'pairs')
+#> pairsFile: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
+#> metadata(0):
+import(pairsFile(coolf), format = 'pairs')
#> GInteractions object with 471364 interactions and 3 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 | frag1 frag2
#> <Rle> <IRanges> <Rle> <IRanges> | <numeric> <numeric>
@@ -313,56 +307,49 @@ Supporting file classes#> [471364] 203
#> -------
#> regions: 549331 ranges and 0 metadata columns
-#> seqinfo: 17 sequences from an unspecified genome
-
-
+#> seqinfo: 17 sequences from an unspecified genome
+
## --- HicFile
hic_file <- HiContactsData('yeast_wt', format = 'hic')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache
-
-hicf <- HicFile(hic_file, pairsFile = pairs_file)
+#> loading from cache
+hicf <- HicFile(hic_file, pairsFile = pairs_file)
hicf
#> HicFile object
-#> .hic file: /github/home/.cache/R/ExperimentHub/f065726fdac_7836
+#> .hic file: /github/home/.cache/R/ExperimentHub/dc2626a16c2_7836
#> resolution: 1000
-#> pairs file: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
-#> metadata(0):
-
-import(hicf)
+#> pairs file: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
+#> metadata(0):
+import(hicf)
#> `HiCExperiment` object with 13,681,280 contacts over 12,165 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f065726fdac_7836"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc2626a16c2_7836"
#> focus: "whole genome"
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 1000
#> interactions: 2965693
#> scores(2): count balanced
#> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
-#> pairsFile: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
-#> metadata(0):
-
-
+#> pairsFile: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
+#> metadata(0):
+
## --- HicproFile
hicpro_matrix_file <- HiContactsData('yeast_wt', format = 'hicpro_matrix')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache
-
-hicpro_regions_file <- HiContactsData('yeast_wt', format = 'hicpro_bed')
+#> loading from cache
+hicpro_regions_file <- HiContactsData('yeast_wt', format = 'hicpro_bed')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache
-
-hicprof <- HicproFile(hicpro_matrix_file, bed = hicpro_regions_file)
+#> loading from cache
+hicprof <- HicproFile(hicpro_matrix_file, bed = hicpro_regions_file)
hicprof
#> HicproFile object
#> HiC-Pro files:
-#> $ matrix: /github/home/.cache/R/ExperimentHub/f0671bb4605_7837
-#> $ regions: /github/home/.cache/R/ExperimentHub/f0613204cac_7838
+#> $ matrix: /github/home/.cache/R/ExperimentHub/dc26515c750_7837
+#> $ regions: /github/home/.cache/R/ExperimentHub/dc25ff90ee1_7838
#> resolution: 1000
#> pairs file:
-#> metadata(0):
-
-import(hicprof)
+#> metadata(0):
+import(hicprof)
#> Registered S3 methods overwritten by 'readr':
#> method from
#> as.data.frame.spec_tbl_df vroom
@@ -375,7 +362,7 @@ Supporting file classes#> str.col_spec vroom
#> `HiCExperiment` object with 9,503,604 contacts over 12,165 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f0671bb4605_7837"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc26515c750_7837"
#> focus: "whole genome"
#> resolutions(1): 1000
#> active resolution: 1000
@@ -394,7 +381,7 @@ Querying subsets of Hi-C matrix f
The focus argument is used to specifically import
contacts within a genomic locus of interest.
-
+
availableChromosomes(cool_file)
#> Seqinfo object with 16 sequences from an unspecified genome:
#> seqnames seqlengths isCircular genome
@@ -408,13 +395,12 @@ Querying subsets of Hi-C matrix f
#> XIII 924431 <NA> <NA>
#> XIV 784333 <NA> <NA>
#> XV 1091291 <NA> <NA>
-#> XVI 948066 <NA> <NA>
-
-hic <- import(cool_file, format = 'cool', focus = 'I:20001-80000')
+#> XVI 948066 <NA> <NA>
+hic <- import(cool_file, format = 'cool', focus = 'I:20001-80000')
hic
#> `HiCExperiment` object with 24,322 contacts over 60 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f065f43dd61_7751"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc2169bc907_7751"
#> focus: "I:20,001-80,000"
#> resolutions(1): 1000
#> active resolution: 1000
@@ -422,9 +408,8 @@ Querying subsets of Hi-C matrix f
#> scores(2): count balanced
#> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
#> pairsFile: N/A
-#> metadata(0):
-
Note:
Querying subsets of HiC-Pro formatted matrices is currently not
@@ -434,7 +419,7 @@
Querying subsets of Hi-C matrix f
not centered at the diagonal. To do this, specify a couple of
coordinates in the focus argument using a character string
formatted as "...|...":
-
+
hic <- import(cool_file, format = 'cool', focus = 'II:1-500000|II:100001-300000')
focus(hic)
#> [1] "II:1-500000|II:100001-300000"
@@ -446,16 +431,14 @@ Multi-resolution Hi-C matrix files.hic files as well: in this case, the user
can specify the resolution at which count values are
recovered.
-
+
mcool_file <- HiContactsData('yeast_wt', format = 'mcool')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache
-
-availableResolutions(mcool_file)
+#> loading from cache
+availableResolutions(mcool_file)
#> resolutions(5): 1000 2000 4000 8000 16000
-#>
-
-availableChromosomes(mcool_file)
+#>
+availableChromosomes(mcool_file)
#> Seqinfo object with 16 sequences from an unspecified genome:
#> seqnames seqlengths isCircular genome
#> I 230218 <NA> <NA>
@@ -468,13 +451,12 @@ Multi-resolution Hi-C matrix files#> XIII 924431 <NA> <NA>
#> XIV 784333 <NA> <NA>
#> XV 1091291 <NA> <NA>
-#> XVI 948066 <NA> <NA>
-
-hic <- import(mcool_file, format = 'cool', focus = 'II:1-800000', resolution = 2000)
+#> XVI 948066 <NA> <NA>
+hic <- import(mcool_file, format = 'cool', focus = 'II:1-800000', resolution = 2000)
hic
#> `HiCExperiment` object with 466,123 contacts over 400 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f0646279c31_7752"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc24e3419b1_7752"
#> focus: "II:1-800,000"
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 2000
@@ -493,20 +475,16 @@ Slots
Slots for a HiCExperiment object can be accessed using
the following getters:
-
+
fileName(hic)
-#> [1] "/github/home/.cache/R/ExperimentHub/f0646279c31_7752"
-
-focus(hic)
-#> [1] "II:1-800000"
-
-resolutions(hic)
-#> [1] 1000 2000 4000 8000 16000
-
-resolution(hic)
-#> [1] 2000
-
-interactions(hic)
+#> [1] "/github/home/.cache/R/ExperimentHub/dc24e3419b1_7752"
+focus(hic)
+#> [1] "II:1-800000"
+resolutions(hic)
+#> [1] 1000 2000 4000 8000 16000
+resolution(hic)
+#> [1] 2000
+interactions(hic)
#> GInteractions object with 33479 interactions and 4 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 | bin_id1
#> <Rle> <IRanges> <Rle> <IRanges> | <numeric>
@@ -536,29 +514,23 @@ Slots
#> [33479] 515 117 0.0536429
#> -------
#> regions: 400 ranges and 4 metadata columns
-#> seqinfo: 16 sequences from an unspecified genome
-
-scores(hic)
+#> seqinfo: 16 sequences from an unspecified genome
+scores(hic)
#> List of length 2
-#> names(2): count balanced
-
-
-tail(scores(hic, 'balanced'))
-#> [1] 0.08204677 0.11941893 0.09562069 0.05017035 0.12493137 0.05364290
-
-topologicalFeatures(hic)
+#> names(2): count balanced
+tail(scores(hic, 1))
+#> [1] 212 309 227 130 297 117
+tail(scores(hic, 'balanced'))
+#> [1] 0.08204677 0.11941893 0.09562069 0.05017035 0.12493137 0.05364290
+topologicalFeatures(hic)
#> List of length 4
-#> names(4): compartments borders loops viewpoints
-
-pairsFile(hic)
-#> NULL
-
-metadata(hic)
+#> names(4): compartments borders loops viewpoints
+pairsFile(hic)
+#> NULL
+metadata(hic)
#> list()
Several extra functions are available as well:
-
+
seqinfo(hic) ## To recover the `Seqinfo` object from the `.(m)cool` file
#> Seqinfo object with 16 sequences from an unspecified genome:
#> seqnames seqlengths isCircular genome
@@ -572,9 +544,8 @@ Slots
#> XIII 924431 <NA> <NA>
#> XIV 784333 <NA> <NA>
#> XV 1091291 <NA> <NA>
-#> XVI 948066 <NA> <NA>
-
-bins(hic) ## To bin the genome at the current resolution
+#> XVI 948066 <NA> <NA>
+bins(hic) ## To bin the genome at the current resolution
#> GRanges object with 6045 ranges and 2 metadata columns:
#> seqnames ranges strand | bin_id weight
#> <Rle> <IRanges> <Rle> | <numeric> <numeric>
@@ -590,9 +561,8 @@ Slots
#> XVI_946001_948000 XVI 946001-948000 * | 6043 NaN
#> XVI_948001_948066 XVI 948001-948066 * | 6044 NaN
#> -------
-#> seqinfo: 16 sequences from an unspecified genome
-
-regions(hic) ## To extract unique regions of the contact matrix
+#> seqinfo: 16 sequences from an unspecified genome
+regions(hic) ## To extract unique regions of the contact matrix
#> GRanges object with 400 ranges and 4 metadata columns:
#> seqnames ranges strand | bin_id weight chr
#> <Rle> <IRanges> <Rle> | <numeric> <numeric> <Rle>
@@ -621,9 +591,8 @@ Slots
#> II_796001_798000 797000
#> II_798001_800000 799000
#> -------
-#> seqinfo: 16 sequences from an unspecified genome
-
-anchors(hic) ## To extract "first" and "second" anchors for each interaction
+#> seqinfo: 16 sequences from an unspecified genome
+anchors(hic) ## To extract "first" and "second" anchors for each interaction
#> $first
#> GRanges object with 33479 ranges and 4 metadata columns:
#> seqnames ranges strand | bin_id weight chr center
@@ -667,13 +636,12 @@ Slot settersScores
Add any scores metric using a numerical vector.
-
+
-
@@ -681,13 +649,12 @@ Features
Add topologicalFeatures using GRanges or
Pairs.
-
+
topologicalFeatures(hic, 'viewpoints') <- GRanges("II:300001-320000")
topologicalFeatures(hic)
#> List of length 4
-#> names(4): compartments borders loops viewpoints
-
-topologicalFeatures(hic, 'viewpoints')
+#> names(4): compartments borders loops viewpoints
+topologicalFeatures(hic, 'viewpoints')
#> GRanges object with 1 range and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
@@ -702,7 +669,7 @@ Coercing HiCExperimentas()
function, HiCExperiment can
be coerced in GInteractions, ContactMatrix and
matrix seamlessly.
-
+
as(hic, "GInteractions")
#> GInteractions object with 33479 interactions and 5 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 | bin_id1
@@ -733,18 +700,16 @@ Coercing HiCExperiment#> [33479] 515 117 0.0536429 0.664753
#> -------
#> regions: 400 ranges and 4 metadata columns
-#> seqinfo: 16 sequences from an unspecified genome
-
-as(hic, "ContactMatrix")
+#> seqinfo: 16 sequences from an unspecified genome
+as(hic, "ContactMatrix")
#> class: ContactMatrix
#> dim: 400 400
#> type: dgCMatrix
#> rownames: NULL
#> colnames: NULL
#> metadata(0):
-#> regions: 400
-
-as(hic, "matrix")[1:10, 1:10]
+#> regions: 400
+as(hic, "matrix")[1:10, 1:10]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> [1,] NaN 0 NaN NaN NaN NaN NaN NaN
#> [2,] 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000
@@ -766,9 +731,8 @@ Coercing HiCExperiment#> [7,] 0.13249106 0.09404388
#> [8,] 0.18151495 0.12720548
#> [9,] 0.06494950 0.11622354
-#> [10,] 0.11622354 0.06796588
-
-as(hic, "data.frame")[1:10, ]
+#> [10,] 0.11622354 0.06796588
+as(hic, "data.frame")[1:10, ]
#> seqnames1 start1 end1 width1 strand1 bin_id1 weight1 center1 seqnames2
#> 1 II 1 2000 2000 * 116 NaN 1000 II
#> 2 II 1 2000 2000 * 116 NaN 1000 II
@@ -824,7 +788,7 @@ Importing pairs files
Pairs in any of these different formats are automatically detected
and imported in R with the import function:
-
+
import(pairs_file, format = 'pairs')
#> GInteractions object with 471364 interactions and 3 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 | frag1 frag2
@@ -867,10 +831,10 @@ Further documentation
Session info
-
+
sessionInfo()
-#> R version 4.4.0 (2024-04-24)
-#> Platform: x86_64-pc-linux-gnu
+#> R version 4.3.3 (2024-02-29)
+#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.4 LTS
#>
#> Matrix products: default
@@ -893,64 +857,67 @@ Session info#> [8] base
#>
#> other attached packages:
-#> [1] HiCExperiment_1.3.1 HiContactsData_1.7.0 ExperimentHub_2.13.0
-#> [4] AnnotationHub_3.13.0 BiocFileCache_2.13.0 dbplyr_2.5.0
-#> [7] GenomicRanges_1.57.0 GenomeInfoDb_1.41.1 IRanges_2.39.0
-#> [10] S4Vectors_0.43.0 BiocGenerics_0.51.0 dplyr_1.1.4
-#> [13] BiocStyle_2.33.0
+#> [1] HiCExperiment_1.3.1 HiContactsData_1.4.0 ExperimentHub_2.10.0
+#> [4] AnnotationHub_3.10.1 BiocFileCache_2.10.2 dbplyr_2.5.0
+#> [7] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 IRanges_2.36.0
+#> [10] S4Vectors_0.40.2 BiocGenerics_0.48.1 dplyr_1.1.4
+#> [13] BiocStyle_2.30.0
#>
#> loaded via a namespace (and not attached):
-#> [1] DBI_1.2.3 rlang_1.1.3
-#> [3] magrittr_2.0.3 matrixStats_1.3.0
-#> [5] compiler_4.4.0 RSQLite_2.3.7
-#> [7] png_0.1-8 systemfonts_1.1.0
-#> [9] vctrs_0.6.5 stringr_1.5.1
-#> [11] pkgconfig_2.0.3 crayon_1.5.2
-#> [13] fastmap_1.2.0 XVector_0.45.0
-#> [15] utf8_1.2.4 rmarkdown_2.27
-#> [17] tzdb_0.4.0 UCSC.utils_1.1.0
-#> [19] ggbeeswarm_0.7.2 strawr_0.0.91
-#> [21] ragg_1.3.2 purrr_1.0.2
-#> [23] bit_4.0.5 xfun_0.44
-#> [25] zlibbioc_1.51.0 cachem_1.1.0
-#> [27] jsonlite_1.8.8 blob_1.2.4
-#> [29] highr_0.11 rhdf5filters_1.17.0
-#> [31] DelayedArray_0.31.1 Rhdf5lib_1.27.0
-#> [33] BiocParallel_1.39.0 parallel_4.4.0
-#> [35] R6_2.5.1 bslib_0.7.0
-#> [37] stringi_1.8.4 jquerylib_0.1.4
-#> [39] Rcpp_1.0.12 bookdown_0.39
-#> [41] SummarizedExperiment_1.35.0 knitr_1.47
-#> [43] readr_2.1.5 Matrix_1.7-0
-#> [45] tidyselect_1.2.1 abind_1.4-5
-#> [47] yaml_2.3.8 codetools_0.2-20
-#> [49] curl_5.2.1 lattice_0.22-6
-#> [51] tibble_3.2.1 InteractionSet_1.33.0
-#> [53] Biobase_2.65.0 withr_3.0.0
-#> [55] KEGGREST_1.45.0 evaluate_0.23
-#> [57] ggrastr_1.0.2 desc_1.4.3
-#> [59] Biostrings_2.73.0 pillar_1.9.0
-#> [61] BiocManager_1.30.23 filelock_1.0.3
-#> [63] MatrixGenerics_1.17.0 generics_0.1.3
-#> [65] vroom_1.6.5 hms_1.1.3
-#> [67] BiocVersion_3.20.0 ggplot2_3.5.1
-#> [69] munsell_0.5.1 scales_1.3.0
-#> [71] glue_1.7.0 tools_4.4.0
-#> [73] BiocIO_1.15.0 RSpectra_0.16-1
-#> [75] fs_1.6.4 rhdf5_2.49.0
-#> [77] grid_4.4.0 tidyr_1.3.1
-#> [79] colorspace_2.1-0 AnnotationDbi_1.67.0
-#> [81] GenomeInfoDbData_1.2.12 beeswarm_0.4.0
-#> [83] vipor_0.4.7 cli_3.6.2
-#> [85] rappdirs_0.3.3 textshaping_0.4.0
-#> [87] fansi_1.0.6 S4Arrays_1.5.1
-#> [89] gtable_0.3.5 HiContacts_1.7.0
-#> [91] sass_0.4.9 digest_0.6.35
-#> [93] SparseArray_1.5.7 htmlwidgets_1.6.4
-#> [95] memoise_2.0.1 htmltools_0.5.8.1
-#> [97] pkgdown_2.0.9 lifecycle_1.0.4
-#> [99] httr_1.4.7 mime_0.12
-#> [101] bit64_4.0.5
+#> [1] DBI_1.2.2 bitops_1.0-7
+#> [3] rlang_1.1.3 magrittr_2.0.3
+#> [5] matrixStats_1.3.0 compiler_4.3.3
+#> [7] RSQLite_2.3.6 png_0.1-8
+#> [9] systemfonts_1.0.6 vctrs_0.6.5
+#> [11] stringr_1.5.1 pkgconfig_2.0.3
+#> [13] crayon_1.5.2 fastmap_1.1.1
+#> [15] XVector_0.42.0 utf8_1.2.4
+#> [17] promises_1.3.0 rmarkdown_2.26
+#> [19] tzdb_0.4.0 ggbeeswarm_0.7.2
+#> [21] strawr_0.0.91 ragg_1.3.0
+#> [23] purrr_1.0.2 bit_4.0.5
+#> [25] xfun_0.43 zlibbioc_1.48.2
+#> [27] cachem_1.0.8 jsonlite_1.8.8
+#> [29] blob_1.2.4 highr_0.10
+#> [31] later_1.3.2 rhdf5filters_1.14.1
+#> [33] DelayedArray_0.28.0 Rhdf5lib_1.24.2
+#> [35] BiocParallel_1.36.0 interactiveDisplayBase_1.40.0
+#> [37] parallel_4.3.3 R6_2.5.1
+#> [39] bslib_0.7.0 stringi_1.8.3
+#> [41] jquerylib_0.1.4 Rcpp_1.0.12
+#> [43] bookdown_0.39 SummarizedExperiment_1.32.0
+#> [45] knitr_1.46 readr_2.1.5
+#> [47] httpuv_1.6.15 Matrix_1.6-5
+#> [49] tidyselect_1.2.1 abind_1.4-5
+#> [51] yaml_2.3.8 codetools_0.2-20
+#> [53] curl_5.2.1 lattice_0.22-6
+#> [55] tibble_3.2.1 InteractionSet_1.30.0
+#> [57] Biobase_2.62.0 shiny_1.8.1.1
+#> [59] withr_3.0.0 KEGGREST_1.42.0
+#> [61] ggrastr_1.0.2 evaluate_0.23
+#> [63] desc_1.4.3 Biostrings_2.70.3
+#> [65] pillar_1.9.0 BiocManager_1.30.22
+#> [67] filelock_1.0.3 MatrixGenerics_1.14.0
+#> [69] generics_0.1.3 vroom_1.6.5
+#> [71] RCurl_1.98-1.14 hms_1.1.3
+#> [73] ggplot2_3.5.0 BiocVersion_3.18.1
+#> [75] munsell_0.5.1 scales_1.3.0
+#> [77] xtable_1.8-4 glue_1.7.0
+#> [79] tools_4.3.3 BiocIO_1.12.0
+#> [81] RSpectra_0.16-1 fs_1.6.3
+#> [83] rhdf5_2.46.1 grid_4.3.3
+#> [85] tidyr_1.3.1 colorspace_2.1-0
+#> [87] AnnotationDbi_1.64.1 GenomeInfoDbData_1.2.11
+#> [89] beeswarm_0.4.0 vipor_0.4.7
+#> [91] cli_3.6.2 rappdirs_0.3.3
+#> [93] textshaping_0.3.7 fansi_1.0.6
+#> [95] S4Arrays_1.2.1 gtable_0.3.5
+#> [97] HiContacts_1.4.0 sass_0.4.9
+#> [99] digest_0.6.35 SparseArray_1.2.4
+#> [101] htmlwidgets_1.6.4 memoise_2.0.1
+#> [103] htmltools_0.5.8.1 pkgdown_2.0.9
+#> [105] lifecycle_1.0.4 httr_1.4.7
+#> [107] mime_0.12 bit64_4.0.5
diff --git a/authors.html b/authors.html
index d7c3517..2edcbcb 100644
--- a/authors.html
+++ b/authors.html
@@ -62,7 +62,7 @@ Citation
doi:10.1038/s41467-024-44761-x.
@Article{,
- author = {Jacqyes Serizay and Cyril Matthey-Doret and Amaury Bignaud and Lyam Baudry and Romain Koszul},
+ author = {Jacques Serizay and Cyril Matthey-Doret and Amaury Bignaud and Lyam Baudry and Romain Koszul},
title = {Orchestrating chromosome conformation capture analysis with Bioconductor},
journal = {Nature Communications},
year = {2024},
diff --git a/pkgdown.yml b/pkgdown.yml
index 9d0b099..e9e27b9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,7 +1,7 @@
-pandoc: '3.2'
+pandoc: 3.1.1
pkgdown: 2.0.9
pkgdown_sha: ~
articles:
HiCExperiment: HiCExperiment.html
-last_built: 2024-06-03T14:47Z
+last_built: 2024-06-03T14:48Z
diff --git a/reference/AggrHiCExperiment.html b/reference/AggrHiCExperiment.html
index 857d36c..9b6bf00 100644
--- a/reference/AggrHiCExperiment.html
+++ b/reference/AggrHiCExperiment.html
@@ -203,7 +203,7 @@ Examplesx
#> `AggrHiCExperiment` object over 2 targets
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f0646279c31_7752"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc24e3419b1_7752"
#> focus: 2 targets
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 8000
diff --git a/reference/CoolFile-class.html b/reference/CoolFile-class.html
index 186419f..1ca5e4c 100644
--- a/reference/CoolFile-class.html
+++ b/reference/CoolFile-class.html
@@ -123,15 +123,15 @@ Examples)
cf
#> CoolFile object
-#> .mcool file: /github/home/.cache/R/ExperimentHub/f0646279c31_7752
+#> .mcool file: /github/home/.cache/R/ExperimentHub/dc24e3419b1_7752
#> resolution: 2000
-#> pairs file: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
+#> pairs file: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
#> metadata(1): info
resolution(cf)
#> [1] 2000
pairsFile(cf)
#> EH7703
-#> "/github/home/.cache/R/ExperimentHub/f0647f3ec13_7753"
+#> "/github/home/.cache/R/ExperimentHub/dc270d70ec4_7753"
metadata(cf)
#> $info
#> [1] "Yeast WT Hi-C exp."
diff --git a/reference/HiCExperiment.html b/reference/HiCExperiment.html
index 8445d85..b4f1d0f 100644
--- a/reference/HiCExperiment.html
+++ b/reference/HiCExperiment.html
@@ -333,14 +333,14 @@ Examplescontacts
#> `HiCExperiment` object with 8,757,906 contacts over 1,517 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f0646279c31_7752"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc24e3419b1_7752"
#> focus: "whole genome"
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 8000
#> interactions: 801962
#> scores(2): count balanced
#> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
-#> pairsFile: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
+#> pairsFile: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
#> metadata(0):
#####################################################################
@@ -367,7 +367,7 @@ Examples#####################################################################
fileName(contacts)
-#> [1] "/github/home/.cache/R/ExperimentHub/f0646279c31_7752"
+#> [1] "/github/home/.cache/R/ExperimentHub/dc24e3419b1_7752"
focus(contacts)
#> NULL
resolutions(contacts)
@@ -413,7 +413,7 @@ Examples#> names(4): compartments borders loops viewpoints
pairsFile(contacts)
#> EH7703
-#> "/github/home/.cache/R/ExperimentHub/f0647f3ec13_7753"
+#> "/github/home/.cache/R/ExperimentHub/dc270d70ec4_7753"
#####################################################################
## ---------------------- Slot getters --------------------------- ##
@@ -450,62 +450,62 @@ Examplescontacts[1:100]
#> `HiCExperiment` object with 4,140 contacts over 100 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f0646279c31_7752"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc24e3419b1_7752"
#> focus: "whole genome"
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 8000
#> interactions: 100
#> scores(3): count balanced random
#> topologicalFeatures: compartments(0) borders(0) loops(1) viewpoints(0)
-#> pairsFile: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
+#> pairsFile: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
#> metadata(0):
contacts['II']
#> `HiCExperiment` object with 471,364 contacts over 102 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f0646279c31_7752"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc24e3419b1_7752"
#> focus: "II"
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 8000
#> interactions: 4693
#> scores(3): count balanced random
#> topologicalFeatures: compartments(0) borders(0) loops(1) viewpoints(0)
-#> pairsFile: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
+#> pairsFile: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
#> metadata(0):
contacts[c('II', 'III')]
#> `HiCExperiment` object with 632,446 contacts over 142 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f0646279c31_7752"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc24e3419b1_7752"
#> focus: "II, III"
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 8000
#> interactions: 8502
#> scores(3): count balanced random
#> topologicalFeatures: compartments(0) borders(0) loops(1) viewpoints(0)
-#> pairsFile: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
+#> pairsFile: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
#> metadata(0):
contacts['II|III']
#> `HiCExperiment` object with 9,092 contacts over 142 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f0646279c31_7752"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc24e3419b1_7752"
#> focus: "II:1-813184|III:1-316620"
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 8000
#> interactions: 3000
#> scores(3): count balanced random
#> topologicalFeatures: compartments(0) borders(0) loops(1) viewpoints(0)
-#> pairsFile: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
+#> pairsFile: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
#> metadata(0):
contacts['II:10001-30000|III:50001-90000']
#> `HiCExperiment` object with 11 contacts over 5 regions
#> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/f0646279c31_7752"
+#> fileName: "/github/home/.cache/R/ExperimentHub/dc24e3419b1_7752"
#> focus: "II:10001-30000|III:50001-90000"
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 8000
#> interactions: 4
#> scores(3): count balanced random
#> topologicalFeatures: compartments(0) borders(0) loops(1) viewpoints(0)
-#> pairsFile: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
+#> pairsFile: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
#> metadata(0):
#####################################################################
diff --git a/reference/HicFile-class.html b/reference/HicFile-class.html
index ac898b4..6c7914a 100644
--- a/reference/HicFile-class.html
+++ b/reference/HicFile-class.html
@@ -117,15 +117,15 @@ Examples)
hic
#> HicFile object
-#> .hic file: /github/home/.cache/R/ExperimentHub/f065726fdac_7836
+#> .hic file: /github/home/.cache/R/ExperimentHub/dc2626a16c2_7836
#> resolution: 16000
-#> pairs file: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
+#> pairs file: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
#> metadata(1): type
resolution(hic)
#> [1] 16000
pairsFile(hic)
#> EH7703
-#> "/github/home/.cache/R/ExperimentHub/f0647f3ec13_7753"
+#> "/github/home/.cache/R/ExperimentHub/dc270d70ec4_7753"
metadata(hic)
#> $type
#> [1] "example"
diff --git a/reference/HicproFile-class.html b/reference/HicproFile-class.html
index 5a79a7a..df20bf4 100644
--- a/reference/HicproFile-class.html
+++ b/reference/HicproFile-class.html
@@ -128,16 +128,16 @@ Exampleshicpro
#> HicproFile object
#> HiC-Pro files:
-#> $ matrix: /github/home/.cache/R/ExperimentHub/f0671bb4605_7837
-#> $ regions: /github/home/.cache/R/ExperimentHub/f0613204cac_7838
+#> $ matrix: /github/home/.cache/R/ExperimentHub/dc26515c750_7837
+#> $ regions: /github/home/.cache/R/ExperimentHub/dc25ff90ee1_7838
#> resolution: 1000
-#> pairs file: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
+#> pairs file: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
#> metadata(1): type
resolution(hicpro)
#> [1] 1000
pairsFile(hicpro)
#> EH7703
-#> "/github/home/.cache/R/ExperimentHub/f0647f3ec13_7753"
+#> "/github/home/.cache/R/ExperimentHub/dc270d70ec4_7753"
metadata(hicpro)
#> $type
#> [1] "example"
diff --git a/reference/PairsFile-class.html b/reference/PairsFile-class.html
index 0b81331..5f9da45 100644
--- a/reference/PairsFile-class.html
+++ b/reference/PairsFile-class.html
@@ -75,10 +75,10 @@ Examplespf <- PairsFile(pairsPath)
pf
#> PairsFile object
-#> resource: /github/home/.cache/R/ExperimentHub/f0647f3ec13_7753
+#> resource: /github/home/.cache/R/ExperimentHub/dc270d70ec4_7753
pairsFile(pf)
#> EH7703
-#> "/github/home/.cache/R/ExperimentHub/f0647f3ec13_7753"
+#> "/github/home/.cache/R/ExperimentHub/dc270d70ec4_7753"