diff --git a/404.html b/404.html index c5429cf..58bd4a6 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/LICENSE-text.html b/LICENSE-text.html index fefac2f..2d348a9 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/LICENSE.html b/LICENSE.html index 1e1bb59..f173a17 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/articles/HiContacts.html b/articles/HiContacts.html index 5ab3a38..812ce9a 100644 --- a/articles/HiContacts.html +++ b/articles/HiContacts.html @@ -32,7 +32,7 @@ HiContacts - 1.5.0 + 1.7.1 @@ -178,7 +178,7 @@

Basics: importin hic #> `HiCExperiment` object with 8,757,906 contacts over 12,079 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/1c7240a87e35_7751" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea709f2aa8_7751" #> focus: "whole genome" #> resolutions(1): 1000 #> active resolution: 1000 @@ -314,7 +314,7 @@

Summing two mapshic_1 #> `HiCExperiment` object with 301,285 contacts over 150 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/1c7211b16995_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea73b99dd3_7754" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 2000 @@ -326,7 +326,7 @@

Summing two mapshic_2 #> `HiCExperiment` object with 146,812 contacts over 150 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_7752" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 2000 @@ -338,7 +338,7 @@

Summing two mapsmerged_hic #> `HiCExperiment` object with 229,926 contacts over 150 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/1c7211b16995_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea73b99dd3_7754" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 2000 @@ -406,7 +406,7 @@

Chromosome compartmentshic #> `HiCExperiment` object with 8,757,906 contacts over 763 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -446,7 +446,7 @@

Diamond insulati hic #> `HiCExperiment` object with 146,812 contacts over 300 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_7752" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 @@ -528,7 +528,7 @@

P(s) #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache ps <- distanceLaw(hic) -#> Importing pairs file /github/home/.cache/R/ExperimentHub/1c72216031c6_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/1bea16b12b37_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 or values outside the scale range #> (`geom_line()`). @@ -562,9 +562,9 @@

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/1c72216031c6_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/1bea16b12b37_7753 in memory. This may take a while... ps_2 <- distanceLaw(c2) |> mutate(sample = 'Eco1-AID') -#> Importing pairs file /github/home/.cache/R/ExperimentHub/1c726989fbd7_7755 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/1bea9aa094d_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 or values outside the scale range @@ -609,7 +609,7 @@

Session info#> [1] InteractionSet_1.33.0 SummarizedExperiment_1.35.2 #> [3] Biobase_2.65.1 MatrixGenerics_1.17.0 #> [5] matrixStats_1.4.1 rtracklayer_1.65.0 -#> [7] HiContacts_1.5.0 HiContactsData_1.7.0 +#> [7] HiContacts_1.7.1 HiContactsData_1.7.0 #> [9] ExperimentHub_2.13.1 AnnotationHub_3.13.3 #> [11] BiocFileCache_2.13.0 dbplyr_2.5.0 #> [13] HiCExperiment_1.5.1 GenomicRanges_1.57.1 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 6dbaf6b..d368103 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 31ae2bd..8fffb83 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 d5c453d..4a07757 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 1e66183..4aecd1a 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 f51be1a..c0cd772 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/articles/index.html b/articles/index.html index 2bd1a8b..9f9bcbc 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/authors.html b/authors.html index c38c3e0..629402e 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/index.html b/index.html index 7434a0b..793b292 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/pkgdown.yml b/pkgdown.yml index 85e9837..8a3e435 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: HiContacts: HiContacts.html -last_built: 2024-09-30T12:12Z +last_built: 2024-09-30T12:23Z diff --git a/reference/Contacts.html b/reference/Contacts.html index d0cbdb4..23a6c5b 100644 --- a/reference/Contacts.html +++ b/reference/Contacts.html @@ -18,7 +18,7 @@ HiContacts - 1.5.0 + 1.7.1 @@ -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/1c7247efb38b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 diff --git a/reference/HiContacts-plots.html b/reference/HiContacts-plots.html index 5cf1dfa..50e2253 100644 --- a/reference/HiContacts-plots.html +++ b/reference/HiContacts-plots.html @@ -24,7 +24,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/Ps.html b/reference/Ps.html index 11adc06..7299d17 100644 --- a/reference/Ps.html +++ b/reference/Ps.html @@ -19,7 +19,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/arithmetics.html b/reference/arithmetics.html index 2356f50..ffb9783 100644 --- a/reference/arithmetics.html +++ b/reference/arithmetics.html @@ -34,7 +34,7 @@ HiContacts - 1.5.0 + 1.7.1 @@ -234,7 +234,7 @@

Examples

#> #> `HiCExperiment` object with 8,757,906 contacts over 763 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_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/1c7247efb38b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_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/1c7247efb38b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_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/1c7211b16995_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea73b99dd3_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/1c7247efb38b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_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/1c7247efb38b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_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/1c7247efb38b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_7752" #> focus: "II" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 diff --git a/reference/checks.html b/reference/checks.html index c966279..9fa5984 100644 --- a/reference/checks.html +++ b/reference/checks.html @@ -19,7 +19,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/cisTransRatio.html b/reference/cisTransRatio.html index 18a356e..d050635 100644 --- a/reference/cisTransRatio.html +++ b/reference/cisTransRatio.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/getCompartments.html b/reference/getCompartments.html index 8641edc..cf5a771 100644 --- a/reference/getCompartments.html +++ b/reference/getCompartments.html @@ -18,7 +18,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/getDiamondInsulation.html b/reference/getDiamondInsulation.html index eca44ad..a8510af 100644 --- a/reference/getDiamondInsulation.html +++ b/reference/getDiamondInsulation.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 @@ -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/1c7247efb38b_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_7752" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 diff --git a/reference/getLoops.html b/reference/getLoops.html index c60f715..c33e867 100644 --- a/reference/getLoops.html +++ b/reference/getLoops.html @@ -20,7 +20,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/index.html b/reference/index.html index d6db1c6..225bed5 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/palettes.html b/reference/palettes.html index 7ddb99b..3db90f1 100644 --- a/reference/palettes.html +++ b/reference/palettes.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/plot4C.html b/reference/plot4C.html index b4c701f..8b5b5e9 100644 --- a/reference/plot4C.html +++ b/reference/plot4C.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/plotMatrix-1.png b/reference/plotMatrix-1.png index d45f4fa..f0a73a3 100644 Binary files a/reference/plotMatrix-1.png and b/reference/plotMatrix-1.png differ diff --git a/reference/plotMatrix.html b/reference/plotMatrix.html index bc05a46..8032de9 100644 --- a/reference/plotMatrix.html +++ b/reference/plotMatrix.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/plotPs.html b/reference/plotPs.html index a1f4a60..37f389a 100644 --- a/reference/plotPs.html +++ b/reference/plotPs.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/plotSaddle.html b/reference/plotSaddle.html index 7811c1c..916f057 100644 --- a/reference/plotSaddle.html +++ b/reference/plotSaddle.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/plotScalogram.html b/reference/plotScalogram.html index 72e0db1..4443d6a 100644 --- a/reference/plotScalogram.html +++ b/reference/plotScalogram.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 @@ -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/1c72216031c6_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/1bea16b12b37_7753 in memory. This may take a while... plotScalogram(scalo) diff --git a/reference/reexports.html b/reference/reexports.html index f498703..b8959c0 100644 --- a/reference/reexports.html +++ b/reference/reexports.html @@ -24,7 +24,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/scalogram.html b/reference/scalogram.html index c608d38..ce06da5 100644 --- a/reference/scalogram.html +++ b/reference/scalogram.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 @@ -93,7 +93,7 @@

Examples

#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache scalo <- scalogram(contacts_yeast['II']) -#> Importing pairs file /github/home/.cache/R/ExperimentHub/1c72216031c6_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/1bea16b12b37_7753 in memory. This may take a while... scalo #> # A tibble: 750 × 4 #> # Groups: chr, binned_pos [250] diff --git a/reference/tracks.html b/reference/tracks.html index 95c668f..bb2056f 100644 --- a/reference/tracks.html +++ b/reference/tracks.html @@ -17,7 +17,7 @@ HiContacts - 1.5.0 + 1.7.1 diff --git a/reference/virtual4C.html b/reference/virtual4C.html index 823769f..6804b4a 100644 --- a/reference/virtual4C.html +++ b/reference/virtual4C.html @@ -18,7 +18,7 @@ HiContacts - 1.5.0 + 1.7.1