diff --git a/articles/HiContacts.html b/articles/HiContacts.html index c075328..4147170 100644 --- a/articles/HiContacts.html +++ b/articles/HiContacts.html @@ -70,7 +70,7 @@

Introduction to HiContacts

Jacques Serizay

-

2023-09-04

+

2023-10-03

Source: vignettes/HiContacts.Rmd @@ -175,7 +175,7 @@

Basics: importin hic #> `HiCExperiment` object with 8,757,906 contacts over 12,079 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47412db9b61_7751" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b39b4c87d_7751" #> focus: "whole genome" #> resolutions(1): 1000 #> active resolution: 1000 @@ -311,7 +311,7 @@

Summing two mapshic_1 #> `HiCExperiment` object with 301,285 contacts over 150 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/474649a1ab5_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1130bf7b_7754" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 2000 @@ -323,7 +323,7 @@

Summing two mapshic_2 #> `HiCExperiment` object with 146,812 contacts over 150 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47414b9f10b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1c8c5bdb_7752" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 2000 @@ -335,7 +335,7 @@

Summing two mapsmerged_hic #> `HiCExperiment` object with 229,926 contacts over 150 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/474649a1ab5_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1130bf7b_7754" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 2000 @@ -403,7 +403,7 @@

Chromosome compartmentshic #> `HiCExperiment` object with 8,757,906 contacts over 763 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47414b9f10b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1c8c5bdb_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -443,7 +443,7 @@

Diamond insulati hic #> `HiCExperiment` object with 146,812 contacts over 300 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47414b9f10b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1c8c5bdb_7752" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 @@ -524,7 +524,7 @@

P(s) #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache ps <- distanceLaw(hic) -#> Importing pairs file /github/home/.cache/R/ExperimentHub/4745df2935f_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/4e2baeaae59_7753 in memory. This may take a while... plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p)) #> Warning: Removed 67 rows containing missing values (`geom_line()`).

@@ -556,9 +556,9 @@

P(s) #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache ps_1 <- distanceLaw(c1) |> mutate(sample = 'WT') -#> Importing pairs file /github/home/.cache/R/ExperimentHub/4745df2935f_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/4e2baeaae59_7753 in memory. This may take a while... ps_2 <- distanceLaw(c2) |> mutate(sample = 'Eco1-AID') -#> Importing pairs file /github/home/.cache/R/ExperimentHub/4742e3edec3_7755 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/4e2b39de5b16_7755 in memory. This may take a while... ps <- rbind(ps_1, ps_2) plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p, group = sample, color = sample)) #> Warning: Removed 134 rows containing missing values (`geom_line()`). @@ -574,9 +574,9 @@

Session info
 sessionInfo()
-#> R version 4.3.0 (2023-04-21)
+#> R version 4.3.1 (2023-06-16)
 #> Platform: x86_64-pc-linux-gnu (64-bit)
-#> Running under: Ubuntu 22.04.2 LTS
+#> Running under: Ubuntu 22.04.3 LTS
 #> 
 #> Matrix products: default
 #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -603,82 +603,82 @@ 
Session info#>  [5] matrixStats_1.0.0           rtracklayer_1.60.1         
 #>  [7] HiContacts_1.3.2            HiContactsData_1.2.0       
 #>  [9] ExperimentHub_2.8.1         AnnotationHub_3.8.0        
-#> [11] BiocFileCache_2.8.0         dbplyr_2.3.3               
+#> [11] BiocFileCache_2.8.0         dbplyr_2.3.4               
 #> [13] HiCExperiment_1.0.0         GenomicRanges_1.52.0       
-#> [15] GenomeInfoDb_1.36.2         IRanges_2.34.1             
-#> [17] S4Vectors_0.38.1            BiocGenerics_0.46.0        
-#> [19] dplyr_1.1.2                 ggplot2_3.4.3              
-#> [21] BiocStyle_2.28.0           
+#> [15] GenomeInfoDb_1.36.3         IRanges_2.34.1             
+#> [17] S4Vectors_0.38.2            BiocGenerics_0.46.0        
+#> [19] dplyr_1.1.3                 ggplot2_3.4.3              
+#> [21] BiocStyle_2.28.1           
 #> 
 #> loaded via a namespace (and not attached):
 #>   [1] strawr_0.0.91                 rstudioapi_0.15.0            
 #>   [3] jsonlite_1.8.7                magrittr_2.0.3               
 #>   [5] ggbeeswarm_0.7.2              farver_2.1.1                 
-#>   [7] rmarkdown_2.24                fs_1.6.3                     
+#>   [7] rmarkdown_2.25                fs_1.6.3                     
 #>   [9] BiocIO_1.10.0                 zlibbioc_1.46.0              
 #>  [11] ragg_1.2.5                    vctrs_0.6.3                  
 #>  [13] memoise_2.0.1                 Cairo_1.6-1                  
 #>  [15] Rsamtools_2.16.0              RCurl_1.98-1.12              
-#>  [17] terra_1.7-39                  base64enc_0.1-3              
+#>  [17] terra_1.7-46                  base64enc_0.1-3              
 #>  [19] htmltools_0.5.6               S4Arrays_1.0.6               
 #>  [21] dynamicTreeCut_1.63-1         curl_5.0.2                   
-#>  [23] Rhdf5lib_1.22.0               Formula_1.2-5                
+#>  [23] Rhdf5lib_1.22.1               Formula_1.2-5                
 #>  [25] rhdf5_2.44.0                  sass_0.4.7                   
 #>  [27] bslib_0.5.1                   htmlwidgets_1.6.2            
 #>  [29] desc_1.4.2                    impute_1.74.1                
 #>  [31] cachem_1.0.8                  GenomicAlignments_1.36.0     
 #>  [33] mime_0.12                     lifecycle_1.0.3              
 #>  [35] iterators_1.0.14              pkgconfig_2.0.3              
-#>  [37] Matrix_1.5-4                  R6_2.5.1                     
+#>  [37] Matrix_1.6-1                  R6_2.5.1                     
 #>  [39] fastmap_1.1.1                 GenomeInfoDbData_1.2.10      
 #>  [41] shiny_1.7.5                   digest_0.6.33                
 #>  [43] colorspace_2.1-0              patchwork_1.1.3              
 #>  [45] AnnotationDbi_1.62.2          rprojroot_2.0.3              
-#>  [47] RSpectra_0.16-1               Hmisc_5.1-0                  
+#>  [47] RSpectra_0.16-1               Hmisc_5.1-1                  
 #>  [49] textshaping_0.3.6             RSQLite_2.3.1                
 #>  [51] filelock_1.0.2                labeling_0.4.3               
 #>  [53] fansi_1.0.4                   httr_1.4.7                   
-#>  [55] abind_1.4-5                   compiler_4.3.0               
-#>  [57] bit64_4.0.5                   withr_2.5.0                  
+#>  [55] abind_1.4-5                   compiler_4.3.1               
+#>  [57] bit64_4.0.5                   withr_2.5.1                  
 #>  [59] doParallel_1.0.17             backports_1.4.1              
 #>  [61] htmlTable_2.4.1               BiocParallel_1.34.2          
-#>  [63] DBI_1.1.3                     highr_0.10                   
-#>  [65] rappdirs_0.3.3                DelayedArray_0.26.7          
-#>  [67] rjson_0.2.21                  tools_4.3.0                  
-#>  [69] foreign_0.8-84                vipor_0.4.5                  
-#>  [71] beeswarm_0.4.0                interactiveDisplayBase_1.38.0
-#>  [73] httpuv_1.6.11                 nnet_7.3-18                  
-#>  [75] glue_1.6.2                    restfulr_0.0.15              
-#>  [77] rhdf5filters_1.12.1           promises_1.2.1               
-#>  [79] grid_4.3.0                    checkmate_2.2.0              
-#>  [81] cluster_2.1.4                 generics_0.1.3               
-#>  [83] gtable_0.3.4                  tzdb_0.4.0                   
-#>  [85] preprocessCore_1.62.1         tidyr_1.3.0                  
-#>  [87] data.table_1.14.8             hms_1.1.3                    
-#>  [89] WGCNA_1.72-1                  utf8_1.2.3                   
-#>  [91] XVector_0.40.0                BiocVersion_3.17.1           
-#>  [93] foreach_1.5.2                 pillar_1.9.0                 
-#>  [95] stringr_1.5.0                 vroom_1.6.3                  
-#>  [97] later_1.3.1                   splines_4.3.0                
-#>  [99] lattice_0.21-8                survival_3.5-5               
-#> [101] bit_4.0.5                     tidyselect_1.2.0             
-#> [103] GO.db_3.17.0                  Biostrings_2.68.1            
-#> [105] knitr_1.43                    gridExtra_2.3                
-#> [107] bookdown_0.35                 xfun_0.40                    
-#> [109] stringi_1.7.12                yaml_2.3.7                   
-#> [111] evaluate_0.21                 codetools_0.2-19             
-#> [113] tibble_3.2.1                  BiocManager_1.30.22          
-#> [115] cli_3.6.1                     rpart_4.1.19                 
-#> [117] xtable_1.8-4                  systemfonts_1.0.4            
-#> [119] munsell_0.5.0                 jquerylib_0.1.4              
-#> [121] Rcpp_1.0.11                   png_0.1-8                    
-#> [123] fastcluster_1.2.3             XML_3.99-0.14                
-#> [125] ggrastr_1.0.2                 parallel_4.3.0               
-#> [127] ellipsis_0.3.2                pkgdown_2.0.7                
-#> [129] readr_2.1.4                   blob_1.2.4                   
-#> [131] bitops_1.0-7                  scales_1.2.1                 
-#> [133] purrr_1.0.2                   crayon_1.5.2                 
-#> [135] rlang_1.1.1                   KEGGREST_1.40.0
+#> [63] DBI_1.1.3 rappdirs_0.3.3 +#> [65] DelayedArray_0.26.7 rjson_0.2.21 +#> [67] tools_4.3.1 foreign_0.8-85 +#> [69] vipor_0.4.5 beeswarm_0.4.0 +#> [71] interactiveDisplayBase_1.38.0 httpuv_1.6.11 +#> [73] nnet_7.3-19 glue_1.6.2 +#> [75] restfulr_0.0.15 rhdf5filters_1.12.1 +#> [77] promises_1.2.1 grid_4.3.1 +#> [79] checkmate_2.2.0 cluster_2.1.4 +#> [81] generics_0.1.3 gtable_0.3.4 +#> [83] tzdb_0.4.0 preprocessCore_1.62.1 +#> [85] tidyr_1.3.0 data.table_1.14.8 +#> [87] hms_1.1.3 WGCNA_1.72-1 +#> [89] utf8_1.2.3 XVector_0.40.0 +#> [91] BiocVersion_3.17.1 foreach_1.5.2 +#> [93] pillar_1.9.0 stringr_1.5.0 +#> [95] vroom_1.6.3 later_1.3.1 +#> [97] splines_4.3.1 lattice_0.21-8 +#> [99] survival_3.5-7 bit_4.0.5 +#> [101] tidyselect_1.2.0 GO.db_3.17.0 +#> [103] Biostrings_2.68.1 knitr_1.44 +#> [105] gridExtra_2.3 bookdown_0.35 +#> [107] xfun_0.40 stringi_1.7.12 +#> [109] yaml_2.3.7 evaluate_0.21 +#> [111] codetools_0.2-19 tibble_3.2.1 +#> [113] BiocManager_1.30.22 cli_3.6.1 +#> [115] rpart_4.1.19 xtable_1.8-4 +#> [117] systemfonts_1.0.4 munsell_0.5.0 +#> [119] jquerylib_0.1.4 Rcpp_1.0.11 +#> [121] png_0.1-8 fastcluster_1.2.3 +#> [123] XML_3.99-0.14 ggrastr_1.0.2 +#> [125] parallel_4.3.1 ellipsis_0.3.2 +#> [127] pkgdown_2.0.7 readr_2.1.4 +#> [129] blob_1.2.4 bitops_1.0-7 +#> [131] scales_1.2.1 purrr_1.0.2 +#> [133] crayon_1.5.2 rlang_1.1.1 +#> [135] KEGGREST_1.40.1 diff --git a/articles/HiContacts_files/figure-html/unnamed-chunk-4-1.png b/articles/HiContacts_files/figure-html/unnamed-chunk-4-1.png index 9d167d9..c696db5 100644 Binary files a/articles/HiContacts_files/figure-html/unnamed-chunk-4-1.png and b/articles/HiContacts_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/articles/HiContacts_files/figure-html/unnamed-chunk-4-2.png b/articles/HiContacts_files/figure-html/unnamed-chunk-4-2.png index 95984fa..a544f06 100644 Binary files a/articles/HiContacts_files/figure-html/unnamed-chunk-4-2.png and b/articles/HiContacts_files/figure-html/unnamed-chunk-4-2.png differ diff --git a/articles/HiContacts_files/figure-html/unnamed-chunk-7-1.png b/articles/HiContacts_files/figure-html/unnamed-chunk-7-1.png index 2f75ba0..76ab3b0 100644 Binary files a/articles/HiContacts_files/figure-html/unnamed-chunk-7-1.png and b/articles/HiContacts_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/articles/HiContacts_files/figure-html/unnamed-chunk-8-1.png b/articles/HiContacts_files/figure-html/unnamed-chunk-8-1.png index eb7baa0..10aa3fa 100644 Binary files a/articles/HiContacts_files/figure-html/unnamed-chunk-8-1.png and b/articles/HiContacts_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/articles/HiContacts_files/figure-html/unnamed-chunk-9-1.png b/articles/HiContacts_files/figure-html/unnamed-chunk-9-1.png index e0d9dbf..b27c0a9 100644 Binary files a/articles/HiContacts_files/figure-html/unnamed-chunk-9-1.png and b/articles/HiContacts_files/figure-html/unnamed-chunk-9-1.png differ diff --git a/pkgdown.yml b/pkgdown.yml index 5891be8..48cea1f 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,7 +1,7 @@ -pandoc: 2.19.2 +pandoc: 3.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: HiContacts: HiContacts.html -last_built: 2023-09-04T11:50Z +last_built: 2023-10-03T09:52Z diff --git a/reference/Contacts.html b/reference/Contacts.html index 035af58..455ad6c 100644 --- a/reference/Contacts.html +++ b/reference/Contacts.html @@ -136,7 +136,7 @@

Examples

#> Warning: `HiContacts::Contacts` is deprecated; see '?HiCExperiment::HiCExperiment' constructor instead. #> `HiCExperiment` object with 8,757,906 contacts over 12,079 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47414b9f10b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1c8c5bdb_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 diff --git a/reference/arithmetics.html b/reference/arithmetics.html index 0894366..ee053fa 100644 --- a/reference/arithmetics.html +++ b/reference/arithmetics.html @@ -234,7 +234,7 @@

Examples

#> #> `HiCExperiment` object with 8,757,906 contacts over 763 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47414b9f10b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1c8c5bdb_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -251,7 +251,7 @@

Examples

detrend(contacts_yeast) #> `HiCExperiment` object with 8,757,906 contacts over 763 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47414b9f10b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1c8c5bdb_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -269,7 +269,7 @@

Examples

#> #> `HiCExperiment` object with 8,757,906 contacts over 763 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47414b9f10b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1c8c5bdb_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -307,7 +307,7 @@

Examples

merge(contacts_yeast_eco1, contacts_yeast) #> `HiCExperiment` object with 733,836.5 contacts over 51 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/474649a1ab5_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1130bf7b_7754" #> focus: "II" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -324,7 +324,7 @@

Examples

despeckle(contacts_yeast) #> `HiCExperiment` object with 471,364 contacts over 51 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47414b9f10b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1c8c5bdb_7752" #> focus: "II" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -349,7 +349,7 @@

Examples

#> Filtering for contacts within provided targets... #> `AggrHiCExperiment` object over 16 targets #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47414b9f10b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1c8c5bdb_7752" #> focus: 16 targets #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 @@ -370,7 +370,7 @@

Examples

boost(contacts, alpha = 1) #> `HiCExperiment` object with 469,569 contacts over 814 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47414b9f10b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1c8c5bdb_7752" #> focus: "II" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 diff --git a/reference/getDiamondInsulation.html b/reference/getDiamondInsulation.html index 3f554e5..a896ec3 100644 --- a/reference/getDiamondInsulation.html +++ b/reference/getDiamondInsulation.html @@ -109,7 +109,7 @@

Examples

#> Annotating diamond score prominence for each window... #> `HiCExperiment` object with 146,812 contacts over 300 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/47414b9f10b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/4e2b1c8c5bdb_7752" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 diff --git a/reference/plotMatrix-1.png b/reference/plotMatrix-1.png index a7b616d..da8b7ca 100644 Binary files a/reference/plotMatrix-1.png and b/reference/plotMatrix-1.png differ diff --git a/reference/plotScalogram.html b/reference/plotScalogram.html index 56131cb..56cb9e2 100644 --- a/reference/plotScalogram.html +++ b/reference/plotScalogram.html @@ -84,7 +84,7 @@

Examples

#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache scalo <- scalogram(contacts_yeast['II']) -#> Importing pairs file /github/home/.cache/R/ExperimentHub/4745df2935f_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/4e2baeaae59_7753 in memory. This may take a while... plotScalogram(scalo) diff --git a/reference/scalogram.html b/reference/scalogram.html index 4b8fa58..71a67f9 100644 --- a/reference/scalogram.html +++ b/reference/scalogram.html @@ -95,7 +95,7 @@

Examples

#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache scalo <- scalogram(contacts_yeast['II']) -#> Importing pairs file /github/home/.cache/R/ExperimentHub/4745df2935f_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/4e2baeaae59_7753 in memory. This may take a while... scalo #> # A tibble: 750 × 4 #> # Groups: chr, binned_pos [250]