diff --git a/articles/HiCExperiment.html b/articles/HiCExperiment.html index 43d750d..3b5f34a 100644 --- a/articles/HiCExperiment.html +++ b/articles/HiCExperiment.html @@ -180,7 +180,7 @@

The HiCExperiment classhic #> `HiCExperiment` object with 8,757,906 contacts over 763 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/4c37933f9a8_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c5a38fba8_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -217,7 +217,7 @@

Import methodsimport(cool_file, format = 'cool') #> `HiCExperiment` object with 8,757,906 contacts over 12,079 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/4c37512b2f83_7751" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c63cf6d8_7751" #> focus: "whole genome" #> resolutions(1): 1000 #> active resolution: 1000 @@ -260,21 +260,21 @@

Supporting file classescoolf <- CoolFile(cool_file, pairsFile = pairs_file) coolf #> CoolFile object -#> .mcool file: /github/home/.cache/R/ExperimentHub/4c37512b2f83_7751 +#> .mcool file: /github/home/.cache/R/ExperimentHub/531c63cf6d8_7751 #> resolution: 1000 -#> pairs file: /github/home/.cache/R/ExperimentHub/4c377c8dc312_7753 +#> pairs file: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(0): import(coolf) #> `HiCExperiment` object with 8,757,906 contacts over 12,079 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/4c37512b2f83_7751" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c63cf6d8_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/4c377c8dc312_7753 +#> pairsFile: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(0): import(pairsFile(coolf), format = 'pairs') #> GInteractions object with 471364 interactions and 3 metadata columns: @@ -315,21 +315,21 @@

Supporting file classeshicf <- HicFile(hic_file, pairsFile = pairs_file) hicf #> HicFile object -#> .hic file: /github/home/.cache/R/ExperimentHub/4c375e363846_7836 +#> .hic file: /github/home/.cache/R/ExperimentHub/531c5c02eeb7_7836 #> resolution: 1000 -#> pairs file: /github/home/.cache/R/ExperimentHub/4c377c8dc312_7753 +#> pairs file: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(0): import(hicf) #> `HiCExperiment` object with 13,681,280 contacts over 12,165 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/4c375e363846_7836" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c5c02eeb7_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/4c377c8dc312_7753 +#> pairsFile: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(0): ## --- HicproFile @@ -343,8 +343,8 @@

Supporting file classeshicprof #> HicproFile object #> HiC-Pro files: -#> $ matrix: /github/home/.cache/R/ExperimentHub/4c37369ebfbe_7837 -#> $ regions: /github/home/.cache/R/ExperimentHub/4c374c23d242_7838 +#> $ matrix: /github/home/.cache/R/ExperimentHub/531c2191a287_7837 +#> $ regions: /github/home/.cache/R/ExperimentHub/531c15d47484_7838 #> resolution: 1000 #> pairs file: #> metadata(0): @@ -361,7 +361,7 @@

Supporting file classes#> str.col_spec vroom #> `HiCExperiment` object with 9,503,604 contacts over 12,165 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/4c37369ebfbe_7837" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c2191a287_7837" #> focus: "whole genome" #> resolutions(1): 1000 #> active resolution: 1000 @@ -399,7 +399,7 @@

Querying subsets of Hi-C matrix f hic #> `HiCExperiment` object with 24,322 contacts over 60 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/4c37512b2f83_7751" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c63cf6d8_7751" #> focus: "I:20,001-80,000" #> resolutions(1): 1000 #> active resolution: 1000 @@ -455,7 +455,7 @@

Multi-resolution Hi-C matrix fileshic #> `HiCExperiment` object with 466,123 contacts over 400 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/4c37933f9a8_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c5a38fba8_7752" #> focus: "II:1-800,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 2000 @@ -476,7 +476,7 @@

Slots the following getters:

 fileName(hic)
-#> [1] "/github/home/.cache/R/ExperimentHub/4c37933f9a8_7752"
+#> [1] "/github/home/.cache/R/ExperimentHub/531c5a38fba8_7752"
 focus(hic)
 #> [1] "II:1-800000"
 resolutions(hic)
@@ -641,7 +641,7 @@ 
Scores
 #> List of length 3
 #> names(3): count balanced random
 tail(scores(hic, 'random'))
-#> [1] 0.07052068 0.36739323 0.90808718 0.51921820 0.02467053 0.99672496
+#> [1] 0.3747048 0.6409972 0.3851203 0.8239471 0.2446326 0.7485730

Features @@ -686,17 +686,17 @@

Coercing HiCExperiment#> [33479] II 798001-800000 --- II 798001-800000 | 515 #> bin_id2 count balanced random #> <numeric> <numeric> <numeric> <numeric> -#> [1] 116 1 NaN 0.0446930 -#> [2] 118 2 NaN 0.1832870 -#> [3] 119 3 NaN 0.9776305 -#> [4] 120 15 NaN 0.0458923 -#> [5] 121 9 NaN 0.8059366 +#> [1] 116 1 NaN 0.2781041 +#> [2] 118 2 NaN 0.6806936 +#> [3] 119 3 NaN 0.2207362 +#> [4] 120 15 NaN 0.3626733 +#> [5] 121 9 NaN 0.0832896 #> ... ... ... ... ... -#> [33475] 514 309 0.1194189 0.3673932 -#> [33476] 515 227 0.0956207 0.9080872 -#> [33477] 514 130 0.0501703 0.5192182 -#> [33478] 515 297 0.1249314 0.0246705 -#> [33479] 515 117 0.0536429 0.9967250 +#> [33475] 514 309 0.1194189 0.640997 +#> [33476] 515 227 0.0956207 0.385120 +#> [33477] 514 130 0.0501703 0.823947 +#> [33478] 515 297 0.1249314 0.244633 +#> [33479] 515 117 0.0536429 0.748573 #> ------- #> regions: 400 ranges and 4 metadata columns #> seqinfo: 16 sequences from an unspecified genome @@ -756,16 +756,16 @@

Coercing HiCExperiment#> 9 18001 20000 2000 * 125 0.02331795 19000 6 NaN #> 10 20001 22000 2000 * 126 0.02241734 21000 5 NaN #> random -#> 1 0.04469295 -#> 2 0.18328703 -#> 3 0.97763052 -#> 4 0.04589231 -#> 5 0.80593657 -#> 6 0.80672971 -#> 7 0.77821892 -#> 8 0.29936647 -#> 9 0.96788381 -#> 10 0.41045590

+#> 1 0.27810409 +#> 2 0.68069356 +#> 3 0.22073618 +#> 4 0.36267331 +#> 5 0.08328962 +#> 6 0.62624774 +#> 7 0.36784233 +#> 8 0.85045007 +#> 9 0.65799371 +#> 10 0.88249176
@@ -857,11 +857,11 @@

Session info#> [8] base #> #> other attached packages: -#> [1] HiCExperiment_1.1.2 HiContactsData_1.2.0 ExperimentHub_2.8.1 -#> [4] AnnotationHub_3.8.0 BiocFileCache_2.8.0 dbplyr_2.3.4 -#> [7] GenomicRanges_1.52.0 GenomeInfoDb_1.36.4 IRanges_2.34.1 -#> [10] S4Vectors_0.38.2 BiocGenerics_0.46.0 dplyr_1.1.3 -#> [13] BiocStyle_2.28.1 +#> [1] HiCExperiment_1.1.2 HiContactsData_1.3.0 ExperimentHub_2.9.1 +#> [4] AnnotationHub_3.9.2 BiocFileCache_2.9.1 dbplyr_2.3.4 +#> [7] GenomicRanges_1.53.1 GenomeInfoDb_1.37.6 IRanges_2.35.2 +#> [10] S4Vectors_0.39.2 BiocGenerics_0.47.0 dplyr_1.1.3 +#> [13] BiocStyle_2.29.2 #> #> loaded via a namespace (and not attached): #> [1] DBI_1.1.3 bitops_1.0-7 @@ -871,53 +871,53 @@

Session info#> [9] systemfonts_1.0.4 vctrs_0.6.3 #> [11] stringr_1.5.0 pkgconfig_2.0.3 #> [13] crayon_1.5.2 fastmap_1.1.1 -#> [15] XVector_0.40.0 ellipsis_0.3.2 +#> [15] XVector_0.41.1 ellipsis_0.3.2 #> [17] utf8_1.2.3 promises_1.2.1 #> [19] rmarkdown_2.25 tzdb_0.4.0 #> [21] ggbeeswarm_0.7.2 strawr_0.0.91 #> [23] ragg_1.2.5 purrr_1.0.2 #> [25] bit_4.0.5 xfun_0.40 -#> [27] zlibbioc_1.46.0 cachem_1.0.8 +#> [27] zlibbioc_1.47.0 cachem_1.0.8 #> [29] jsonlite_1.8.7 blob_1.2.4 -#> [31] later_1.3.1 rhdf5filters_1.12.1 -#> [33] DelayedArray_0.26.7 Rhdf5lib_1.22.1 -#> [35] BiocParallel_1.34.2 interactiveDisplayBase_1.38.0 +#> [31] later_1.3.1 rhdf5filters_1.13.5 +#> [33] DelayedArray_0.27.10 Rhdf5lib_1.23.2 +#> [35] BiocParallel_1.35.4 interactiveDisplayBase_1.39.0 #> [37] parallel_4.3.1 R6_2.5.1 #> [39] bslib_0.5.1 stringi_1.7.12 #> [41] jquerylib_0.1.4 Rcpp_1.0.11 -#> [43] bookdown_0.35 SummarizedExperiment_1.30.2 +#> [43] bookdown_0.35 SummarizedExperiment_1.31.1 #> [45] knitr_1.44 readr_2.1.4 -#> [47] httpuv_1.6.11 Matrix_1.6-1 +#> [47] httpuv_1.6.11 Matrix_1.6-1.1 #> [49] tidyselect_1.2.0 abind_1.4-5 #> [51] yaml_2.3.7 codetools_0.2-19 #> [53] curl_5.1.0 lattice_0.21-8 -#> [55] tibble_3.2.1 InteractionSet_1.28.1 -#> [57] Biobase_2.60.0 shiny_1.7.5 -#> [59] withr_2.5.1 KEGGREST_1.40.1 +#> [55] tibble_3.2.1 withr_2.5.1 +#> [57] InteractionSet_1.29.1 Biobase_2.61.0 +#> [59] shiny_1.7.5 KEGGREST_1.41.4 #> [61] ggrastr_1.0.2 evaluate_0.22 -#> [63] desc_1.4.2 Biostrings_2.68.1 +#> [63] desc_1.4.2 Biostrings_2.69.2 #> [65] pillar_1.9.0 BiocManager_1.30.22 -#> [67] filelock_1.0.2 MatrixGenerics_1.12.3 +#> [67] filelock_1.0.2 MatrixGenerics_1.13.1 #> [69] generics_0.1.3 vroom_1.6.4 #> [71] rprojroot_2.0.3 RCurl_1.98-1.12 #> [73] hms_1.1.3 ggplot2_3.4.3 -#> [75] BiocVersion_3.17.1 munsell_0.5.0 +#> [75] BiocVersion_3.18.0 munsell_0.5.0 #> [77] scales_1.2.1 xtable_1.8-4 #> [79] glue_1.6.2 tools_4.3.1 -#> [81] BiocIO_1.10.0 RSpectra_0.16-1 -#> [83] fs_1.6.3 rhdf5_2.44.0 +#> [81] BiocIO_1.11.0 RSpectra_0.16-1 +#> [83] fs_1.6.3 rhdf5_2.45.1 #> [85] grid_4.3.1 tidyr_1.3.0 -#> [87] colorspace_2.1-0 AnnotationDbi_1.62.2 +#> [87] colorspace_2.1-0 AnnotationDbi_1.63.2 #> [89] GenomeInfoDbData_1.2.10 beeswarm_0.4.0 #> [91] vipor_0.4.5 cli_3.6.1 #> [93] rappdirs_0.3.3 textshaping_0.3.6 -#> [95] fansi_1.0.4 S4Arrays_1.0.6 -#> [97] gtable_0.3.4 HiContacts_1.2.0 +#> [95] fansi_1.0.4 S4Arrays_1.1.6 +#> [97] gtable_0.3.4 HiContacts_1.3.2 #> [99] sass_0.4.7 digest_0.6.33 -#> [101] memoise_2.0.1 htmltools_0.5.6 -#> [103] pkgdown_2.0.7 lifecycle_1.0.3 -#> [105] httr_1.4.7 mime_0.12 -#> [107] bit64_4.0.5

+#> [101] SparseArray_1.1.12 memoise_2.0.1 +#> [103] htmltools_0.5.6 pkgdown_2.0.7 +#> [105] lifecycle_1.0.3 httr_1.4.7 +#> [107] mime_0.12 bit64_4.0.5 diff --git a/pkgdown.yml b/pkgdown.yml index 11dca99..9a36ec1 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: HiCExperiment: HiCExperiment.html -last_built: 2023-10-04T18:25Z +last_built: 2023-10-04T18:27Z diff --git a/reference/AggrHiCExperiment.html b/reference/AggrHiCExperiment.html index 09f2ee1..f038767 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/4c37933f9a8_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c5a38fba8_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 5b77609..660b454 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/4c37933f9a8_7752 +#> .mcool file: /github/home/.cache/R/ExperimentHub/531c5a38fba8_7752 #> resolution: 2000 -#> pairs file: /github/home/.cache/R/ExperimentHub/4c377c8dc312_7753 +#> pairs file: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(1): info resolution(cf) #> [1] 2000 pairsFile(cf) #> EH7703 -#> "/github/home/.cache/R/ExperimentHub/4c377c8dc312_7753" +#> "/github/home/.cache/R/ExperimentHub/531c2e393b5f_7753" metadata(cf) #> $info #> [1] "Yeast WT Hi-C exp." diff --git a/reference/HiCExperiment.html b/reference/HiCExperiment.html index eacb719..fae2ca4 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/4c37933f9a8_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c5a38fba8_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/4c377c8dc312_7753 +#> pairsFile: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(0): ##################################################################### @@ -367,7 +367,7 @@

Examples##################################################################### fileName(contacts) -#> [1] "/github/home/.cache/R/ExperimentHub/4c37933f9a8_7752" +#> [1] "/github/home/.cache/R/ExperimentHub/531c5a38fba8_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/4c377c8dc312_7753" +#> "/github/home/.cache/R/ExperimentHub/531c2e393b5f_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/4c37933f9a8_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c5a38fba8_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/4c377c8dc312_7753 +#> pairsFile: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(0): contacts['II'] #> `HiCExperiment` object with 471,364 contacts over 102 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/4c37933f9a8_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c5a38fba8_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/4c377c8dc312_7753 +#> pairsFile: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(0): contacts[c('II', 'III')] #> `HiCExperiment` object with 632,446 contacts over 142 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/4c37933f9a8_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c5a38fba8_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/4c377c8dc312_7753 +#> pairsFile: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(0): contacts['II|III'] #> `HiCExperiment` object with 9,092 contacts over 142 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/4c37933f9a8_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c5a38fba8_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/4c377c8dc312_7753 +#> pairsFile: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(0): contacts['II:10001-30000|III:50001-90000'] #> `HiCExperiment` object with 11 contacts over 5 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/4c37933f9a8_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/531c5a38fba8_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/4c377c8dc312_7753 +#> pairsFile: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(0): ##################################################################### @@ -633,17 +633,17 @@

Examples#> [801962] XVI 936001-944000 --- XVI 936001-944000 | 1515 #> bin_id2 count balanced random #> <numeric> <numeric> <numeric> <numeric> -#> [1] 0 705 0.582493 0.151647 -#> [2] 1 1260 0.935951 0.992425 -#> [3] 2 557 0.294491 0.335782 -#> [4] 3 274 0.174475 0.964701 -#> [5] 4 291 0.138932 0.760817 +#> [1] 0 705 0.582493 0.96712143 +#> [2] 1 1260 0.935951 0.00808371 +#> [3] 2 557 0.294491 0.99680495 +#> [4] 3 274 0.174475 0.38091260 +#> [5] 4 291 0.138932 0.53245652 #> ... ... ... ... ... -#> [801958] 1514 893 0.515549 0.00248225 -#> [801959] 1515 524 0.275326 0.92986403 -#> [801960] 1514 1317 0.728102 0.08272007 -#> [801961] 1515 1582 0.795995 0.98929852 -#> [801962] 1515 1409 0.645227 0.25332382 +#> [801958] 1514 893 0.515549 0.622549 +#> [801959] 1515 524 0.275326 0.930700 +#> [801960] 1514 1317 0.728102 0.460301 +#> [801961] 1515 1582 0.795995 0.425483 +#> [801962] 1515 1409 0.645227 0.597501 #> ------- #> regions: 1517 ranges and 4 metadata columns #> seqinfo: 16 sequences from an unspecified genome diff --git a/reference/HicFile-class.html b/reference/HicFile-class.html index dff919b..a7d88d2 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/4c375e363846_7836 +#> .hic file: /github/home/.cache/R/ExperimentHub/531c5c02eeb7_7836 #> resolution: 16000 -#> pairs file: /github/home/.cache/R/ExperimentHub/4c377c8dc312_7753 +#> pairs file: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(1): type resolution(hic) #> [1] 16000 pairsFile(hic) #> EH7703 -#> "/github/home/.cache/R/ExperimentHub/4c377c8dc312_7753" +#> "/github/home/.cache/R/ExperimentHub/531c2e393b5f_7753" metadata(hic) #> $type #> [1] "example" diff --git a/reference/HicproFile-class.html b/reference/HicproFile-class.html index ed2c366..8cb69f8 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/4c37369ebfbe_7837 -#> $ regions: /github/home/.cache/R/ExperimentHub/4c374c23d242_7838 +#> $ matrix: /github/home/.cache/R/ExperimentHub/531c2191a287_7837 +#> $ regions: /github/home/.cache/R/ExperimentHub/531c15d47484_7838 #> resolution: 1000 -#> pairs file: /github/home/.cache/R/ExperimentHub/4c377c8dc312_7753 +#> pairs file: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 #> metadata(1): type resolution(hicpro) #> [1] 1000 pairsFile(hicpro) #> EH7703 -#> "/github/home/.cache/R/ExperimentHub/4c377c8dc312_7753" +#> "/github/home/.cache/R/ExperimentHub/531c2e393b5f_7753" metadata(hicpro) #> $type #> [1] "example" diff --git a/reference/PairsFile-class.html b/reference/PairsFile-class.html index 435f23f..e1201dc 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/4c377c8dc312_7753 +#> resource: /github/home/.cache/R/ExperimentHub/531c2e393b5f_7753 pairsFile(pf) #> EH7703 -#> "/github/home/.cache/R/ExperimentHub/4c377c8dc312_7753" +#> "/github/home/.cache/R/ExperimentHub/531c2e393b5f_7753"