From 7eae0da06ad9f1f8666487efdcff82af10adc827 Mon Sep 17 00:00:00 2001 From: js2264 Date: Mon, 3 Jun 2024 14:51:18 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20js2264/H?= =?UTF-8?q?iCExperiment@d5702078746526df5157192f2960d1cec42b5e81=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/HiCExperiment.html | 355 ++++++++++++++----------------- authors.html | 2 +- pkgdown.yml | 4 +- reference/AggrHiCExperiment.html | 2 +- reference/CoolFile-class.html | 6 +- reference/HiCExperiment.html | 28 +-- reference/HicFile-class.html | 6 +- reference/HicproFile-class.html | 8 +- reference/PairsFile-class.html | 4 +- reference/data.html | 2 +- reference/import-methods.html | 6 +- reference/subset_chrII.cool | Bin 42795 -> 42795 bytes search.json | 2 +- 13 files changed, 196 insertions(+), 229 deletions(-) diff --git a/articles/HiCExperiment.html b/articles/HiCExperiment.html index ad1b684..62f5b69 100644 --- a/articles/HiCExperiment.html +++ b/articles/HiCExperiment.html @@ -173,16 +173,14 @@

The 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):

-
-focus(hic)
+#> metadata(0):
+focus(hic)
 #> [1] "I:20001-80000"

 
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, 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)
+#> 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.

-
+
 scores(hic, 'random') <- runif(length(hic))
 scores(hic)
 #> List of length 3
-#> names(3): count balanced random

-
-tail(scores(hic, 'random'))
+#> names(3): count balanced random
+tail(scores(hic, 'random'))
 #> [1] 0.1763631 0.7045936 0.2742455 0.9619072 0.8252395 0.6647535

 

 

@@ -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"