diff --git a/articles/HiContacts.html b/articles/HiContacts.html index cbc85e3..f08c0b2 100644 --- a/articles/HiContacts.html +++ b/articles/HiContacts.html @@ -70,7 +70,7 @@

Introduction to HiContacts

Jacques Serizay

-

2023-11-16

+

2023-11-21

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/bc973259915f_7751" +#> fileName: "/github/home/.cache/R/ExperimentHub/8eca3e17cc_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/bc972a75ca39_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec673256d7_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/bc9727d3c305_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec33e709d8_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/bc972a75ca39_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec673256d7_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/bc9727d3c305_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec33e709d8_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/bc9727d3c305_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec33e709d8_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/bc97216e65f_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/8ec7975dcee_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/bc97216e65f_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/8ec7975dcee_7753 in memory. This may take a while... ps_2 <- distanceLaw(c2) |> mutate(sample = 'Eco1-AID') -#> Importing pairs file /github/home/.cache/R/ExperimentHub/bc977c59dfd0_7755 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/8ec6a73345b_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()`). @@ -574,7 +574,7 @@

Session info
 sessionInfo()
-#> R Under development (unstable) (2023-11-08 r85496)
+#> R Under development (unstable) (2023-11-14 r85524)
 #> Platform: x86_64-pc-linux-gnu
 #> Running under: Ubuntu 22.04.3 LTS
 #> 
@@ -607,7 +607,7 @@ 
Session info#> [13] HiCExperiment_1.3.0         GenomicRanges_1.55.1       
 #> [15] GenomeInfoDb_1.39.1         IRanges_2.37.0             
 #> [17] S4Vectors_0.41.1            BiocGenerics_0.49.1        
-#> [19] dplyr_1.1.3                 ggplot2_3.4.4              
+#> [19] dplyr_1.1.4                 ggplot2_3.4.4              
 #> [21] BiocStyle_2.31.0           
 #> 
 #> loaded via a namespace (and not attached):
@@ -673,10 +673,10 @@ 
Session info#> [119] fs_1.6.3                      ggbeeswarm_0.7.2             
 #> [121] stringi_1.8.1                 WGCNA_1.72-1                 
 #> [123] BiocParallel_1.37.0           munsell_0.5.0                
-#> [125] Biostrings_2.71.1             Matrix_1.6-2                 
+#> [125] Biostrings_2.71.1             Matrix_1.6-3                 
 #> [127] hms_1.1.3                     patchwork_1.1.3              
 #> [129] bit64_4.0.5                   Rhdf5lib_1.25.0              
-#> [131] KEGGREST_1.43.0               shiny_1.7.5.1                
+#> [131] KEGGREST_1.43.0               shiny_1.8.0                  
 #> [133] interactiveDisplayBase_1.41.0 highr_0.10                   
 #> [135] memoise_2.0.1                 bslib_0.5.1                  
 #> [137] bit_4.0.5
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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/bc9727d3c305_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec33e709d8_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 388a2eb..b004e4a 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/bc9727d3c305_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec33e709d8_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/bc9727d3c305_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec33e709d8_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/bc9727d3c305_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec33e709d8_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/bc972a75ca39_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec673256d7_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/bc9727d3c305_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec33e709d8_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/bc9727d3c305_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec33e709d8_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/bc9727d3c305_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec33e709d8_7752" #> focus: "II" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 diff --git a/reference/getDiamondInsulation.html b/reference/getDiamondInsulation.html index 4d9fba9..f0695d5 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/bc9727d3c305_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/8ec33e709d8_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 83bd83c..a3ddaf9 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 5d72ec7..29ec1e1 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/bc97216e65f_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/8ec7975dcee_7753 in memory. This may take a while... plotScalogram(scalo) diff --git a/reference/scalogram.html b/reference/scalogram.html index 39a1e7b..323910d 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/bc97216e65f_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/8ec7975dcee_7753 in memory. This may take a while... scalo #> # A tibble: 750 × 4 #> # Groups: chr, binned_pos [250]