diff --git a/404.html b/404.html index 535147a..c5429cf 100644 --- a/404.html +++ b/404.html @@ -18,7 +18,7 @@ - +
- +
@@ -88,16 +88,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/LICENSE-text.html b/LICENSE-text.html index 905685c..fefac2f 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -3,7 +3,7 @@ - +
- +
@@ -65,15 +65,15 @@

License

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/LICENSE.html b/LICENSE.html index fdac5ab..1e1bb59 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -3,7 +3,7 @@ - +
- +
@@ -69,15 +69,15 @@

MIT License

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/articles/HiContacts.html b/articles/HiContacts.html index 54b970e..5ab3a38 100644 --- a/articles/HiContacts.html +++ b/articles/HiContacts.html @@ -12,14 +12,13 @@ - - +
- +
@@ -70,9 +69,9 @@

Introduction to HiContacts

Jacques Serizay

-

2024-06-03

+

2024-09-30

- Source: vignettes/HiContacts.Rmd + Source: vignettes/HiContacts.Rmd
@@ -123,9 +122,8 @@

Basics: importin #> Attaching package: 'rtracklayer' #> The following object is masked from 'package:AnnotationHub': #> -#> hubUrl

-
-library(InteractionSet)
+#>     hubUrl
+library(InteractionSet)
 #> Loading required package: SummarizedExperiment
 #> Loading required package: MatrixGenerics
 #> Loading required package: matrixStats
@@ -172,17 +170,15 @@ 
Basics: importin
 #>     cache
 #> The following object is masked from 'package:AnnotationHub':
 #> 
-#>     cache
-
-cool_file <- HiContactsData('yeast_wt', format = 'cool')
+#>     cache
+cool_file <- HiContactsData('yeast_wt', format = 'cool')
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache
-
-hic <- import(cool_file, format = 'cool')
+#> loading from cache
+hic <- import(cool_file, format = 'cool')
 hic
 #> `HiCExperiment` object with 8,757,906 contacts over 12,079 regions 
 #> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/11307a68a0ec_7751" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7240a87e35_7751" 
 #> focus: "whole genome" 
 #> resolutions(1): 1000
 #> active resolution: 1000 
@@ -206,11 +202,11 @@ 
Plot matrix heatmapsplotMatrix() simply takes the
 first scores available.

-
+
 ## Square matrix
 plotMatrix(hic, use.scores = 'balanced', limits = c(-4, -1))

 

-
+
 
 ## Horizontal matrix
 plotMatrix(
@@ -231,12 +227,11 @@ 
Plot loopsInteractionSet::makeGInteractionsFromGRangesPairs()
 function.

-
+
 mcool_file <- HiContactsData('yeast_wt', format = 'mcool')
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache

-
-loops <- system.file("extdata", 'S288C-loops.bedpe', package = 'HiCExperiment') |> 
+#> loading from cache
+loops <- system.file("extdata", 'S288C-loops.bedpe', package = 'HiCExperiment') |> 
     import() |> 
     makeGInteractionsFromGRangesPairs()
 p <- import(mcool_file, format = 'mcool', focus = 'IV') |> 
@@ -245,7 +240,7 @@ 
Plot loops
 
Plot borders
 

-
+
 borders <- system.file("extdata", 'S288C-borders.bed', package = 'HiCExperiment') |> 
     import()
 p <- import(mcool_file, format = 'mcool', focus = 'IV') |> 
@@ -254,16 +249,15 @@ 
Plot borders
 
Plot aggregated matrices over features
 

-
+
 aggr_centros <- HiContacts::aggregate(
     hic, targets = loops, BPPARAM = BiocParallel::SerialParam()
 )
 #> Going through preflight checklist...
 #> Parsing the entire contact matrice as a sparse matrix...
 #> Modeling distance decay...
-#> Filtering for contacts within provided targets...

-
-plotMatrix(
+#> Filtering for contacts within provided targets...
+plotMatrix(
     aggr_centros, use.scores = 'detrended', limits = c(-1, 1), scale = 'linear', 
     cmap = bgrColors()
 )

@@ -276,30 +270,26 @@ 
Arithmetics
 
Computing autocorrelated contact map
 

-
+
 mcool_file <- HiContactsData('mESCs', format = 'mcool')
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache

-
-hic <- import(mcool_file, format = 'mcool', focus = 'chr2', resolution = 160000)
+#> loading from cache
+hic <- import(mcool_file, format = 'mcool', focus = 'chr2', resolution = 160000)
 hic <- autocorrelate(hic)
-#> 

-
-scores(hic)
+#> 
+scores(hic)
 #> List of length 5
-#> names(5): count balanced expected detrended autocorrelated

-
-summary(scores(hic, 'autocorrelated'))
+#> names(5): count balanced expected detrended autocorrelated
+summary(scores(hic, 'autocorrelated'))
 #>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
-#>  -0.499  -0.097   0.040   0.043   0.172   1.000    7739

-
-plotMatrix(hic, use.scores = 'autocorrelated', limits = c(-1, 1), scale = 'linear')

+#>  -0.499  -0.097   0.040   0.043   0.172   1.000    7739
+plotMatrix(hic, use.scores = 'autocorrelated', limits = c(-1, 1), scale = 'linear')

 

 

 

 
Detrending contact map (map of scores over expected)
 

-
+
 hic <- import(mcool_file, format = 'mcool', focus = 'chr18:20000000-35000000', resolution = 40000)
 detrended_hic <- detrend(hic)
 patchwork::wrap_plots(
@@ -311,22 +301,20 @@ 
Detrending contact m
 

 
Summing two maps
 

-
+
 mcool_file_1 <- HiContactsData('yeast_eco1', format = 'mcool')
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache

-
-mcool_file_2 <- HiContactsData('yeast_wt', format = 'mcool')
+#> loading from cache
+mcool_file_2 <- HiContactsData('yeast_wt', format = 'mcool')
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache

-
-hic_1 <- import(mcool_file_1, format = 'mcool', focus = 'II:1-300000', resolution = 2000)
+#> loading from cache
+hic_1 <- import(mcool_file_1, format = 'mcool', focus = 'II:1-300000', resolution = 2000)
 hic_2 <- import(mcool_file_2, format = 'mcool', focus = 'II:1-300000', resolution = 2000)
 merged_hic <- merge(hic_1, hic_2) 
 hic_1
 #> `HiCExperiment` object with 301,285 contacts over 150 regions 
 #> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/113048cd88ef_7754" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7211b16995_7754" 
 #> focus: "II:1-300,000" 
 #> resolutions(5): 1000 2000 4000 8000 16000
 #> active resolution: 2000 
@@ -334,12 +322,11 @@ 
Summing two maps#> scores(2): count balanced 
 #> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0) 
 #> pairsFile: N/A 
-#> metadata(0):

-
-
-merged_hic
+#> metadata(0):
+merged_hic
 #> `HiCExperiment` object with 229,926 contacts over 150 regions 
 #> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/113048cd88ef_7754" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7211b16995_7754" 
 #> focus: "II:1-300,000" 
 #> resolutions(5): 1000 2000 4000 8000 16000
 #> active resolution: 2000 
@@ -365,7 +351,7 @@ 
Summing two maps
 
Computing ratio between two maps
 

-
+
 hic_1 <- import(mcool_file_1, format = 'mcool', focus = 'II', resolution = 2000)
 hic_2 <- import(mcool_file_2, format = 'mcool', focus = 'II', resolution = 2000)
 div_hic <- divide(hic_1, by = hic_2) 
@@ -380,9 +366,8 @@ 
Computing ratio between two maps#> scores(6): count.x balanced.x count.by balanced.by balanced.fc balanced.l2fc 
 #> topologicalFeatures: () 
 #> pairsFile: N/A 
-#> metadata(2): hce_list operation

-
-p <- patchwork::wrap_plots(
+#> metadata(2): hce_list operation
+p <- patchwork::wrap_plots(
     plotMatrix(hic_1, use.scores = 'balanced', scale = 'log10', limits = c(-4, -1)),
     plotMatrix(hic_2, use.scores = 'balanced', scale = 'log10', limits = c(-4, -1)),
     plotMatrix(div_hic, use.scores = 'balanced.fc', scale = 'log2', limits = c(-2, 2), cmap = bwrColors())
@@ -391,7 +376,7 @@ 
Computing ratio between two maps
 
Despeckling (smoothing out) a contact map
 

-
+
 hic_1_despeckled <- despeckle(hic_1)
 hic_1_despeckled5 <- despeckle(hic_1, focal.size = 5)
 p <- patchwork::wrap_plots(
@@ -407,23 +392,21 @@ 
Mapping topological features
 
Chromosome compartments
 

-
+
 mcool_file <- HiContactsData('yeast_wt', format = 'mcool')
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache

-
-hic <- import(mcool_file, format = 'mcool', resolution = 16000)
+#> loading from cache
+hic <- import(mcool_file, format = 'mcool', resolution = 16000)
 
 # - Get compartments
 hic <- getCompartments(hic, chromosomes = c('XV', 'XVI'))
 #> Going through preflight checklist...
 #> Parsing intra-chromosomal contacts for each chromosome...
-#> Computing eigenvectors for each chromosome...

-
-hic
+#> Computing eigenvectors for each chromosome...
+hic
 #> `HiCExperiment` object with 8,757,906 contacts over 763 regions 
 #> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/11307d784c99_7752" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_7752" 
 #> focus: "whole genome" 
 #> resolutions(5): 1000 2000 4000 8000 16000
 #> active resolution: 16000 
@@ -431,9 +414,8 @@ 
Chromosome compartments#> scores(2): count balanced 
 #> topologicalFeatures: compartments(18) borders(0) loops(0) viewpoints(0) 
 #> pairsFile: N/A 
-#> metadata(1): eigens

-
-
+#> metadata(1): eigens
+
 # - Export compartments as bigwig and bed files
 export(IRanges::coverage(metadata(hic)$eigens, weight = 'eigen'), 'compartments.bw')
 export(
@@ -452,7 +434,7 @@ 
Chromosome compartments
 
Diamond insulation score and chromatin domains borders
 

-
+
 # - Compute insulation score
 hic <- refocus(hic, 'II:1-300000') |> 
     zoom(resolution = 1000) |> 
@@ -460,12 +442,11 @@ 
Diamond insulati
     getBorders()
 #> Going through preflight checklist...
 #> Scan each window and compute diamond insulation score...
-#> Annotating diamond score prominence for each window...

-
-hic
+#> Annotating diamond score prominence for each window...
+hic
 #> `HiCExperiment` object with 146,812 contacts over 300 regions 
 #> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/11307d784c99_7752" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_7752" 
 #> focus: "II:1-300,000" 
 #> resolutions(5): 1000 2000 4000 8000 16000
 #> active resolution: 1000 
@@ -473,9 +454,8 @@ 
Diamond insulati
 #> scores(2): count balanced 
 #> topologicalFeatures: compartments(18) borders(17) loops(0) viewpoints(0) 
 #> pairsFile: N/A 
-#> metadata(2): eigens insulation

-
-
+#> metadata(2): eigens insulation
+
 # - Export insulation as bigwig track and borders as bed file
 export(IRanges::coverage(metadata(hic)$insulation, weight = 'insulation'), 'insulation.bw')
 export(topologicalFeatures(hic, 'borders'), 'borders.bed')

@@ -487,12 +467,11 @@ 
Contact map analysis
 
Virtual 4C
 

-
+
 mcool_file <- HiContactsData('mESCs', format = 'mcool')
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache

-
-hic <- import(mcool_file, format = 'mcool', focus = 'chr18:20000000-35000000', resolution = 40000)
+#> loading from cache
+hic <- import(mcool_file, format = 'mcool', focus = 'chr18:20000000-35000000', resolution = 40000)
 v4C <- virtual4C(hic, viewpoint = GRanges('chr18:31000000-31050000'))
 plot4C(v4C, ggplot2::aes(x = center, y = score))

 

@@ -500,12 +479,11 @@ 
Virtual 4C
 
Cis-trans ratios
 

-
+
 mcool_file <- HiContactsData('yeast_wt', format = 'mcool')
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache

-
-hic <- import(mcool_file, format = 'mcool', resolution = 1000)
+#> loading from cache
+hic <- import(mcool_file, format = 'mcool', resolution = 1000)
 cisTransRatio(hic)
 #> # A tibble: 16 × 6
 #> # Groups:   chr [16]
@@ -531,40 +509,36 @@ 
Cis-trans ratios
 
P(s)
 

-
+
 # Without a pairs file
 mcool_file <- HiContactsData('yeast_wt', format = 'mcool')
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache

-
-hic <- import(mcool_file, format = 'mcool', resolution = 1000)
+#> loading from cache
+hic <- import(mcool_file, format = 'mcool', resolution = 1000)
 ps <- distanceLaw(hic)
-#> pairsFile not specified. The P(s) curve will be an approximation.

-
-plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p))
+#> pairsFile not specified. The P(s) curve will be an approximation.
+plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p))
 #> Warning: Removed 18 rows containing missing values or values outside the scale range
 #> (`geom_line()`).

 

-
+
 
 # With a pairs file
 pairsFile(hic) <- HiContactsData('yeast_wt', format = 'pairs.gz')
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache

-
-ps <- distanceLaw(hic)
-#> Importing pairs file /github/home/.cache/R/ExperimentHub/11301f395da_7753 in memory. This may take a while...

-
-plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p))
+#> loading from cache
+ps <- distanceLaw(hic)
+#> Importing pairs file /github/home/.cache/R/ExperimentHub/1c72216031c6_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()`).

 

-
+
 plotPsSlope(ps, ggplot2::aes(x = binned_distance, y = slope))
 #> Warning: Removed 67 rows containing missing values or values outside the scale range
 #> (`geom_line()`).

 

-
+
 
 # Comparing P(s) curves
 c1 <- import(
@@ -576,9 +550,8 @@ 
P(s)
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
 #> loading from cache
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache

-
-c2 <- import(
+#> loading from cache
+c2 <- import(
     HiContactsData('yeast_eco1', format = 'mcool'), 
     format = 'mcool',
     resolution = 1000, 
@@ -587,20 +560,17 @@ 
P(s)
 #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
 #> loading from cache
 #> 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/11301f395da_7753 in memory. This may take a while...

-
-ps_2 <- distanceLaw(c2) |> mutate(sample = 'Eco1-AID')
-#> Importing pairs file /github/home/.cache/R/ExperimentHub/113077ca2ef5_7755 in memory. This may take a while...

-
-ps <- rbind(ps_1, ps_2)
+#> 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...
+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...
+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
 #> (`geom_line()`).

 

-
+
 plotPsSlope(ps, ggplot2::aes(x = binned_distance, y = slope, group = sample, color = sample))
 #> Warning: Removed 135 rows containing missing values or values outside the scale range
 #> (`geom_line()`).

@@ -610,11 +580,11 @@ 
P(s)
 

 
Session info
 

-
+
 sessionInfo()
-#> R version 4.4.0 (2024-04-24)
+#> R version 4.4.1 (2024-06-14)
 #> Platform: x86_64-pc-linux-gnu
-#> Running under: Ubuntu 22.04.4 LTS
+#> Running under: Ubuntu 22.04.5 LTS
 #> 
 #> Matrix products: default
 #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -636,71 +606,69 @@ 
Session info#> [8] base     
 #> 
 #> other attached packages:
-#>  [1] InteractionSet_1.33.0       SummarizedExperiment_1.35.0
-#>  [3] Biobase_2.65.0              MatrixGenerics_1.17.0      
-#>  [5] matrixStats_1.3.0           rtracklayer_1.65.0         
+#>  [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       
-#>  [9] ExperimentHub_2.13.0        AnnotationHub_3.13.0       
+#>  [9] ExperimentHub_2.13.1        AnnotationHub_3.13.3       
 #> [11] BiocFileCache_2.13.0        dbplyr_2.5.0               
-#> [13] HiCExperiment_1.5.0         GenomicRanges_1.57.0       
-#> [15] GenomeInfoDb_1.41.1         IRanges_2.39.0             
-#> [17] S4Vectors_0.43.0            BiocGenerics_0.51.0        
+#> [13] HiCExperiment_1.5.1         GenomicRanges_1.57.1       
+#> [15] GenomeInfoDb_1.41.1         IRanges_2.39.2             
+#> [17] S4Vectors_0.43.2            BiocGenerics_0.51.2        
 #> [19] dplyr_1.1.4                 ggplot2_3.5.1              
-#> [21] BiocStyle_2.33.0           
+#> [21] BiocStyle_2.33.1           
 #> 
 #> loaded via a namespace (and not attached):
-#>   [1] strawr_0.0.91            rstudioapi_0.16.0        jsonlite_1.8.8          
+#>   [1] strawr_0.0.92            rstudioapi_0.16.0        jsonlite_1.8.9          
 #>   [4] magrittr_2.0.3           ggbeeswarm_0.7.2         farver_2.1.2            
-#>   [7] rmarkdown_2.27           fs_1.6.4                 BiocIO_1.15.0           
-#>  [10] zlibbioc_1.51.0          ragg_1.3.2               vctrs_0.6.5             
-#>  [13] memoise_2.0.1            Cairo_1.6-2              Rsamtools_2.21.0        
-#>  [16] RCurl_1.98-1.14          terra_1.7-78             base64enc_0.1-3         
-#>  [19] htmltools_0.5.8.1        S4Arrays_1.5.1           dynamicTreeCut_1.63-1   
-#>  [22] curl_5.2.1               Rhdf5lib_1.27.0          Formula_1.2-5           
-#>  [25] SparseArray_1.5.7        rhdf5_2.49.0             sass_0.4.9              
-#>  [28] bslib_0.7.0              htmlwidgets_1.6.4        desc_1.4.3              
+#>   [7] rmarkdown_2.28           fs_1.6.4                 BiocIO_1.15.2           
+#>  [10] zlibbioc_1.51.1          ragg_1.3.3               vctrs_0.6.5             
+#>  [13] memoise_2.0.1            Cairo_1.6-2              Rsamtools_2.21.2        
+#>  [16] RCurl_1.98-1.16          terra_1.7-78             base64enc_0.1-3         
+#>  [19] htmltools_0.5.8.1        S4Arrays_1.5.9           dynamicTreeCut_1.63-1   
+#>  [22] curl_5.2.3               Rhdf5lib_1.27.0          Formula_1.2-5           
+#>  [25] SparseArray_1.5.41       rhdf5_2.49.0             sass_0.4.9              
+#>  [28] bslib_0.8.0              htmlwidgets_1.6.4        desc_1.4.3              
 #>  [31] impute_1.79.0            cachem_1.1.0             GenomicAlignments_1.41.0
 #>  [34] mime_0.12                lifecycle_1.0.4          iterators_1.0.14        
 #>  [37] pkgconfig_2.0.3          Matrix_1.7-0             R6_2.5.1                
-#>  [40] fastmap_1.2.0            GenomeInfoDbData_1.2.12  digest_0.6.35           
-#>  [43] colorspace_2.1-0         patchwork_1.2.0          AnnotationDbi_1.67.0    
-#>  [46] RSpectra_0.16-1          Hmisc_5.1-3              textshaping_0.4.0       
+#>  [40] fastmap_1.2.0            GenomeInfoDbData_1.2.12  digest_0.6.37           
+#>  [43] colorspace_2.1-1         patchwork_1.3.0          AnnotationDbi_1.67.0    
+#>  [46] RSpectra_0.16-2          Hmisc_5.1-3              textshaping_0.4.0       
 #>  [49] RSQLite_2.3.7            filelock_1.0.3           labeling_0.4.3          
-#>  [52] fansi_1.0.6              httr_1.4.7               abind_1.4-5             
-#>  [55] compiler_4.4.0           bit64_4.0.5              withr_3.0.0             
-#>  [58] doParallel_1.0.17        backports_1.5.0          htmlTable_2.4.2         
+#>  [52] fansi_1.0.6              httr_1.4.7               abind_1.4-8             
+#>  [55] compiler_4.4.1           bit64_4.5.2              withr_3.0.1             
+#>  [58] doParallel_1.0.17        backports_1.5.0          htmlTable_2.4.3         
 #>  [61] BiocParallel_1.39.0      DBI_1.2.3                highr_0.11              
-#>  [64] rappdirs_0.3.3           DelayedArray_0.31.1      rjson_0.2.21            
-#>  [67] tools_4.4.0              foreign_0.8-86           vipor_0.4.7             
+#>  [64] rappdirs_0.3.3           DelayedArray_0.31.12     rjson_0.2.23            
+#>  [67] tools_4.4.1              foreign_0.8-87           vipor_0.4.7             
 #>  [70] beeswarm_0.4.0           nnet_7.3-19              glue_1.7.0              
-#>  [73] restfulr_0.0.15          rhdf5filters_1.17.0      grid_4.4.0              
-#>  [76] checkmate_2.3.1          cluster_2.1.6            generics_0.1.3          
-#>  [79] gtable_0.3.5             tzdb_0.4.0               preprocessCore_1.67.0   
-#>  [82] tidyr_1.3.1              data.table_1.15.4        hms_1.1.3               
-#>  [85] WGCNA_1.72-5             utf8_1.2.4               XVector_0.45.0          
+#>  [73] restfulr_0.0.15          rhdf5filters_1.17.0      grid_4.4.1              
+#>  [76] checkmate_2.3.2          cluster_2.1.6            generics_0.1.3          
+#>  [79] gtable_0.3.5             tzdb_0.4.0               preprocessCore_1.67.1   
+#>  [82] tidyr_1.3.1              data.table_1.16.0        hms_1.1.3               
+#>  [85] WGCNA_1.73               utf8_1.2.4               XVector_0.45.0          
 #>  [88] BiocVersion_3.20.0       foreach_1.5.2            pillar_1.9.0            
-#>  [91] stringr_1.5.1            vroom_1.6.5              splines_4.4.0           
-#>  [94] lattice_0.22-6           survival_3.6-4           bit_4.0.5               
-#>  [97] tidyselect_1.2.1         GO.db_3.19.1             Biostrings_2.73.0       
-#> [100] knitr_1.47               gridExtra_2.3            bookdown_0.39           
-#> [103] xfun_0.44                stringi_1.8.4            UCSC.utils_1.1.0        
-#> [106] yaml_2.3.8               evaluate_0.23            codetools_0.2-20        
-#> [109] tibble_3.2.1             BiocManager_1.30.23      cli_3.6.2               
+#>  [91] stringr_1.5.1            vroom_1.6.5              splines_4.4.1           
+#>  [94] lattice_0.22-6           survival_3.7-0           bit_4.5.0               
+#>  [97] tidyselect_1.2.1         GO.db_3.20.0             Biostrings_2.73.2       
+#> [100] knitr_1.48               gridExtra_2.3            bookdown_0.40           
+#> [103] xfun_0.47                stringi_1.8.4            UCSC.utils_1.1.0        
+#> [106] yaml_2.3.10              evaluate_1.0.0           codetools_0.2-20        
+#> [109] tibble_3.2.1             BiocManager_1.30.25      cli_3.6.3               
 #> [112] rpart_4.1.23             systemfonts_1.1.0        munsell_0.5.1           
-#> [115] jquerylib_0.1.4          Rcpp_1.0.12              png_0.1-8               
-#> [118] fastcluster_1.2.6        XML_3.99-0.16.1          ggrastr_1.0.2           
-#> [121] parallel_4.4.0           pkgdown_2.0.9            readr_2.1.5             
-#> [124] blob_1.2.4               bitops_1.0-7             scales_1.3.0            
-#> [127] purrr_1.0.2              crayon_1.5.2             rlang_1.1.3             
-#> [130] KEGGREST_1.45.0

+#> [115] jquerylib_0.1.4          Rcpp_1.0.13              png_0.1-8               
+#> [118] fastcluster_1.2.6        XML_3.99-0.17            ggrastr_1.0.2           
+#> [121] parallel_4.4.1           pkgdown_2.1.1            readr_2.1.5             
+#> [124] blob_1.2.4               bitops_1.0-8             scales_1.3.0            
+#> [127] purrr_1.0.2              crayon_1.5.3             rlang_1.1.4             
+#> [130] KEGGREST_1.45.1

 

   

 
   
+      

 
 

 
@@ -713,16 +681,16 @@ 
Session info
   

-
Site built with pkgdown 2.0.9.

+
Site built with pkgdown 2.1.1.

 

 
       
 

 
-  
 
 
-  
+
+
 
   
 
diff --git a/articles/HiContacts_files/figure-html/unnamed-chunk-4-1.png b/articles/HiContacts_files/figure-html/unnamed-chunk-4-1.png
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diff --git a/articles/index.html b/articles/index.html
index 4c31907..2bd1a8b 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -62,15 +62,15 @@ 
All vignettes

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/authors.html b/authors.html
index 54d7f68..c38c3e0 100644
--- a/authors.html
+++ b/authors.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -47,7 +47,7 @@
         
Authors and Citation

       

 
-      
+
       
  • 
           
    Jacques Serizay. Author, maintainer. 
           
    
@@ -56,7 +56,7 @@ 
    Authors and Citation
    
     
    
     
    
       
    Citation
    
-      Source: inst/CITATION
+      Source: inst/CITATION
     
    
     
    
 
@@ -64,7 +64,7 @@ 
    Citation
    
     
    Serizay J, Matthey-Doret C, Bignaud A, Baudry L, Koszul R (2024).
 “Orchestrating chromosome conformation capture analysis with Bioconductor.”
 Nature Communications, 15, 1–9.
-doi:10.1038/s41467-024-44761-x. 
+doi:10.1038/s41467-024-44761-x.
 
    
     
    @Article{,
   author = {Jacques Serizay and Cyril Matthey-Doret and Amaury Bignaud and Lyam Baudry and Romain Koszul},
@@ -87,15 +87,15 @@ 
    Citation
    
 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/index.html b/index.html
index 9a10bae..7434a0b 100644
--- a/index.html
+++ b/index.html
@@ -19,7 +19,7 @@
 
 
 
-    
+
 
     

       

 
 
-      
+
 
       

   

@@ -71,6 +71,9 @@
 
HiContacts
 

 
👉 OHCA book 📖

+
Please cite:

+
Serizay J, Matthey-Doret C, Bignaud A, Baudry L, Koszul R (2024). “Orchestrating chromosome conformation capture analysis with Bioconductor.” Nature Communications, 15, 1-9. doi:10.1038/s41467-024-44761-x.

+
DOI

 

 
HiContacts provides tools to investigate (m)cool matrices imported in R by HiCExperiment.

 
It leverages the HiCExperiment class of objects, built on pre-existing Bioconductor objects, namely InteractionSet, GInterations and ContactMatrix (Lun, Perry & Ing-Simmons, F1000Research 2016), and provides analytical and visualization tools to investigate contact maps.

@@ -335,16 +338,16 @@ 
Dev status

 
 

   

-
Site built with pkgdown 2.0.9.

+
Site built with pkgdown 2.1.1.

 

 
       
 

 
-  
 
 
-  
+
+
 
   
 
diff --git a/pkgdown.yml b/pkgdown.yml
index 7dfe463..85e9837 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,7 +1,6 @@
-pandoc: '3.2'
-pkgdown: 2.0.9
+pandoc: '3.4'
+pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   HiContacts: HiContacts.html
-last_built: 2024-06-03T15:13Z
-
+last_built: 2024-09-30T12:12Z
diff --git a/reference/Contacts.html b/reference/Contacts.html
index 18f66ae..d0cbdb4 100644
--- a/reference/Contacts.html
+++ b/reference/Contacts.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Contacts

-    Source: R/contacts.R
+    Source: R/contacts.R
     
     

 
@@ -70,38 +70,38 @@ 
Contacts

 
     

     
Arguments

-    
file

+
+
+
file

 
Path to a (m)cool file

 
 
-
resolution

+
resolution

 
Resolution to use with mcool file

 
 
-
focus

+
focus

 
focus Chr. coordinates for which
 interaction counts are extracted from the .(m)cool file, provided
 as a character string (e.g. "II:4001-5000"). If not provided,
 the entire (m)cool file will be imported.

 
 
-
metadata

+
metadata

 
list of metadata

 
 
-
topologicalFeatures

+
topologicalFeatures

 
topologicalFeatures provided as a named SimpleList

 
 
-
pairsFile

+
pairsFile

 
Path to an associated .pairs file

 
 

     

     
Value

-    
-
-
a new HiCExperiment object.

+    
a new HiCExperiment object.

     

 
     

@@ -124,8 +124,8 @@ 
Examples

 #>     as.data.frame, basename, cbind, colnames, dirname, do.call,
 #>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
 #>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
-#>     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
-#>     union, unique, unsplit, which.max, which.min
+#>     pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
+#>     tapply, union, unique, unsplit, which.max, which.min
 #> Loading required package: AnnotationHub
 #> Loading required package: BiocFileCache
 #> Loading required package: dbplyr
@@ -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/11307d784c99_7752" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_7752" 
 #> focus: "whole genome" 
 #> resolutions(5): 1000 2000 4000 8000 16000
 #> active resolution: 1000 
@@ -159,15 +159,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/HiContacts-plots.html b/reference/HiContacts-plots.html
index dc2c864..5cf1dfa 100644
--- a/reference/HiContacts-plots.html
+++ b/reference/HiContacts-plots.html
@@ -10,7 +10,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
HiContacts plotting functionalities

-    Source: R/plotting.R
+    Source: R/plotting.R
     
     

 
@@ -77,15 +77,15 @@ 
HiContacts plotting functionalities

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/Ps.html b/reference/Ps.html
index 4ef05f0..11adc06 100644
--- a/reference/Ps.html
+++ b/reference/Ps.html
@@ -5,7 +5,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Compute the law of distance-dependent contact frequency, a.k.a. P(s)

-    Source: R/AllGenerics.R, R/Ps.R
+    Source: R/AllGenerics.R, R/Ps.R
     
     

 
@@ -59,17 +59,17 @@ 
Compute the law of distance-dependent contact frequency, a.k.a. P(s)

     

     
distanceLaw(x, coords, ...)
 
-# S4 method for GInteractions,missing
+# S4 method for class 'GInteractions,missing'
 distanceLaw(x, by_chr = FALSE)
 
-# S4 method for HiCExperiment,missing
+# S4 method for class 'HiCExperiment,missing'
 distanceLaw(
   x,
   by_chr = FALSE,
   filtered_chr = c("XII", "chrXII", "chr12", "12", "Mito", "MT", "chrM")
 )
 
-# S4 method for PairsFile,missing
+# S4 method for class 'PairsFile,missing'
 distanceLaw(
   x,
   by_chr = FALSE,
@@ -77,10 +77,10 @@ 
Compute the law of distance-dependent contact frequency, a.k.a. P(s)

   chunk_size = 1e+05
 )
 
-# S4 method for HiCExperiment,GRanges
+# S4 method for class 'HiCExperiment,GRanges'
 distanceLaw(x, coords, chunk_size = 1e+05)
 
-# S4 method for PairsFile,GRanges
+# S4 method for class 'PairsFile,GRanges'
 distanceLaw(x, coords, chunk_size = 1e+05)
 
 localDistanceLaw(x, coords = coords)

@@ -88,36 +88,36 @@ 
Compute the law of distance-dependent contact frequency, a.k.a. P(s)

 
     

     
Arguments

-    
x

+
+
+
x

 
A HiCExperiment object

 
 
-
coords

+
coords

 
GRanges to specify which genomic loci to use when computing P(s)

 
 
-
...

+
...

 
Arguments passed to corresponding method

 
 
-
by_chr

+
by_chr

 
by_chr

 
 
-
filtered_chr

+
filtered_chr

 
filtered_chr

 
 
-
chunk_size

+
chunk_size

 
For pairs files which do not fit in memory, pick a number
 of pairs to parse by chunks (1e7 should be a good compromise)

 
 

     

     
Value

-    
-
-
a tibble

+    
a tibble

     

 
     

@@ -178,15 +178,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/arithmetics.html b/reference/arithmetics.html
index a24fea7..2356f50 100644
--- a/reference/arithmetics.html
+++ b/reference/arithmetics.html
@@ -20,7 +20,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
HiContacts arithmetics functionalities

-    Source: R/aggregate.R, R/arithmetics.R, R/boost.R, and 3 more
+    Source: R/aggregate.R, R/arithmetics.R, R/boost.R, and 3 more
     
     

 
@@ -84,7 +84,7 @@ 
HiContacts arithmetics functionalities

 

 
     

-    
# S4 method for HiCExperiment
+    
# S4 method for class 'HiCExperiment'
 aggregate(
   x,
   targets,
@@ -99,7 +99,7 @@ 
HiContacts arithmetics functionalities

 
 divide(x, by, use.scores = "balanced", pseudocount = 0)
 
-# S4 method for HiCExperiment,HiCExperiment
+# S4 method for class 'HiCExperiment,HiCExperiment'
 merge(x, y, ..., use.scores = "balanced", FUN = mean)
 
 despeckle(x, use.scores = "balanced", focal.size = 1)
@@ -108,7 +108,7 @@ 
HiContacts arithmetics functionalities

 
 coarsen(x, bin.size)
 
-# S4 method for HiCExperiment
+# S4 method for class 'HiCExperiment'
 normalize(
   object,
   use.scores = "count",
@@ -122,102 +122,102 @@ 
HiContacts arithmetics functionalities

 
     

     
Arguments

-    
x, y, object

+
+
+
x, y, object

 
a HiCExperiment object

 
 
-
targets

+
targets

 
Set of chromosome coordinates for which
 interaction counts are extracted from the Hi-C contact file, provided
 as a GRanges object (for diagnoal-centered loci) or as a GInteractions
 object (for off-diagonal coordinates).

 
 
-
flankingBins

+
flankingBins

 
Number of bins on each flank of the bins containing
 input targets.

 
 
-
maxDistance

+
maxDistance

 
Maximum distance to use when compiling distance decay

 
 
-
BPPARAM

+
BPPARAM

 
BiocParallel parameters

 
 
-
use.scores

+
use.scores

 
Which scores to use to perform operations

 
 
-
detrend

+
detrend

 
Detrend matrix before performing autocorrelation

 
 
-
ignore_ndiags

+
ignore_ndiags

 
ignore N diagonals when calculating correlations

 
 
-
by

+
by

 
a HiCExperiment object

 
 
-
pseudocount

+
pseudocount

 
Add a pseudocount when dividing matrices (Default: 0)

 
 
-
...

+
...

 
HiCExperiment objects. For aggregate, targets (a set of
 GRanges or GInteractions).

 
 
-
FUN

+
FUN

 
merging function

 
 
-
focal.size

+
focal.size

 
Size of the smoothing rectangle

 
 
-
alpha

+
alpha

 
Power law scaling factor. As indicated in Boost-HiC documentation,
 the alpha parameter influences the weighting of contacts: if alpha < 1
 long-range interactions are prioritized; if alpha >> 1 short-range
 interactions have more weight when computing the distance matrix.

 
 
-
full.replace

+
full.replace

 
Whether to replace the entire set of contacts,
 rather than only filling the missing interactions (count=0) (Default: FALSE)

 
 
-
bin.size

+
bin.size

 
Bin size to coarsen a HiCExperiment at

 
 
-
niters

+
niters

 
Number of iterations for ICE matrix balancing

 
 
-
min.nnz

+
min.nnz

 
Filter bins with less than min.nnz non-zero elements when
 performing ICE matrix balancing

 
 
-
mad.max

+
mad.max

 
Filter out bins whose log coverage is less than mad.max
 median absolute deviations below the median bin log coverage.

 
 
-
prop

+
prop

 
Float between 0 and 1, or integer corresponding to the # of

 
 

     

     
Value

-    
-
-
a HiCExperiment object with extra scores

+    
a HiCExperiment object with extra scores

     

 
     

@@ -234,7 +234,7 @@ 
Examples

 #> 
 #> `HiCExperiment` object with 8,757,906 contacts over 763 regions 
 #> -------
-#> fileName: "/github/home/.cache/R/ExperimentHub/11307d784c99_7752" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_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/11307d784c99_7752" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_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/11307d784c99_7752" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_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/113048cd88ef_7754" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7211b16995_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/11307d784c99_7752" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_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/11307d784c99_7752" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_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/11307d784c99_7752" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_7752" 
 #> focus: "II" 
 #> resolutions(5): 1000 2000 4000 8000 16000
 #> active resolution: 1000 
@@ -400,15 +400,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/checks.html b/reference/checks.html
index d9e08a6..c966279 100644
--- a/reference/checks.html
+++ b/reference/checks.html
@@ -5,7 +5,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Checks functions

-    Source: R/checks.R
+    Source: R/checks.R
     
     

 
@@ -74,19 +74,19 @@ 
Checks functions

 
     

     
Arguments

-    
x

+
+
+
x

 
A HiCExperiment object

 
 
-
...

+
...

 
HiCExperiment objects

 
 

     

     
Value

-    
-
-
Logical

+    
Logical

     

 
   

@@ -101,15 +101,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/cisTransRatio.html b/reference/cisTransRatio.html
index 9193e6f..18a356e 100644
--- a/reference/cisTransRatio.html
+++ b/reference/cisTransRatio.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
cisTransRatio

-    Source: R/cistrans.R
+    Source: R/cistrans.R
     
     

 
@@ -58,15 +58,15 @@ 
cisTransRatio

 
     

     
Arguments

-    
x

+
+
+
x

 
A HiCExperiment object over the full genome

 
 

     

     
Value

-    
-
-
a tibble, listing for each chr. the % of cis/trans interactions

+    
a tibble, listing for each chr. the % of cis/trans interactions

     

 
     

@@ -110,15 +110,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/getCompartments.html b/reference/getCompartments.html
index 1264ab0..8641edc 100644
--- a/reference/getCompartments.html
+++ b/reference/getCompartments.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Contact map compartments

-    Source: R/compartments.R
+    Source: R/compartments.R
     
     

 
@@ -68,40 +68,40 @@ 
Contact map compartments

 
     

     
Arguments

-    
x

+
+
+
x

 
A HiCExperiment object over a full genome

 
 
-
resolution

+
resolution

 
Which resolution to use to compute eigen vectors

 
 
-
genome

+
genome

 
a BSgenome of DNAStringSet object associated with the Hi-C
 contact matrix.

 
 
-
chromosomes

+
chromosomes

 
character or integer vector indicating which

 
 
-
neigens

+
neigens

 
Numver of eigen vectors to extract

 
 
-
sort_eigens

+
sort_eigens

 
Can be FALSE or one of c('Spearman', 'Pearson')

 
 
-
BPPARAM

+
BPPARAM

 
BiocParallel parallelization settings

 
 

     

     
Value

-    
-
-
A HiCExperiment object with additional eigens metadata containing the
+    
A HiCExperiment object with additional eigens metadata containing the
 normalized eigenvectors and a new "compartments" topologicalFeatures
 storing A and B compartments as a GRanges object.

     

@@ -173,15 +173,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/getDiamondInsulation.html b/reference/getDiamondInsulation.html
index be5ca46..eca44ad 100644
--- a/reference/getDiamondInsulation.html
+++ b/reference/getDiamondInsulation.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Contact map insulation

-    Source: R/diamond.R
+    Source: R/diamond.R
     
     

 
@@ -60,34 +60,34 @@ 
Contact map insulation

 
     

     
Arguments

-    
x

+
+
+
x

 
A HiCExperiment object over a full genome

 
 
-
window_size

+
window_size

 
Which window size to use to compute diamond insulation
 score (default: 10 * resolution)

 
 
-
BPPARAM

+
BPPARAM

 
BiocParallel parallelization settings

 
 
-
weak_threshold

+
weak_threshold

 
Less stringent cutoff to call borders in the
 diamond insulation score

 
 
-
strong_threshold

+
strong_threshold

 
More stringent cutoff to call borders in the
 diamond insulation score

 
 

     

     
Value

-    
-
-
a HiCExperiment object with additional insulation metadata,
+    
a HiCExperiment object with additional insulation metadata,
 containing the diamond insulation score computed

     

 
@@ -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/11307d784c99_7752" 
+#> fileName: "/github/home/.cache/R/ExperimentHub/1c7247efb38b_7752" 
 #> focus: "II:1-300,000" 
 #> resolutions(5): 1000 2000 4000 8000 16000
 #> active resolution: 1000 
@@ -132,15 +132,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/getLoops.html b/reference/getLoops.html
index c9419ab..c60f715 100644
--- a/reference/getLoops.html
+++ b/reference/getLoops.html
@@ -6,7 +6,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Finding loops in contact map

-    Source: R/loops.R
+    Source: R/loops.R
     
     

 
@@ -64,7 +64,9 @@ 
Finding loops in contact map

 
     

     
Arguments

-    
...

+
+
+
...

 
Parameters passed to HiCool::getLoops().

 
 

@@ -81,15 +83,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/index.html b/reference/index.html
index 346892a..d6db1c6 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -1,9 +1,9 @@
 
-Function reference • HiContactsPackage index • HiContacts
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -131,15 +131,15 @@ 
All functions 
 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/palettes.html b/reference/palettes.html
index 7972370..7ddb99b 100644
--- a/reference/palettes.html
+++ b/reference/palettes.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Matrix palettes

-    Source: R/plotting.R
+    Source: R/plotting.R
     
     

 
@@ -68,9 +68,7 @@ 
Matrix palettes

 
     

     
Value

-    
-
-
A vector of colours carefully
+    
A vector of colours carefully
 picked for Hi-C contact heatmaps

     

 
@@ -106,15 +104,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/plot4C-1.png b/reference/plot4C-1.png
index ae61a6c..081a0f3 100644
Binary files a/reference/plot4C-1.png and b/reference/plot4C-1.png differ
diff --git a/reference/plot4C.html b/reference/plot4C.html
index ca67a90..b4c701f 100644
--- a/reference/plot4C.html
+++ b/reference/plot4C.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Plotting virtual 4C profiles

-    Source: R/plotting.R
+    Source: R/plotting.R
     
     

 
@@ -58,20 +58,20 @@ 
Plotting virtual 4C profiles

 
     

     
Arguments

-    
x

+
+
+
x

 
GRanges, generally the output of virtual4C()

 
 
-
mapping

+
mapping

 
aes to pass on to ggplot2 (default:
 ggplot2::aes(x = center, y = score, col = seqnames))

 
 

     

     
Value

-    
-
-
ggplot

+    
ggplot

     

 
     

@@ -96,15 +96,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/plotMatrix-1.png b/reference/plotMatrix-1.png
index 67e1ba2..d45f4fa 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 4109549..bc05a46 100644
--- a/reference/plotMatrix.html
+++ b/reference/plotMatrix.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Plotting a contact matrix

-    Source: R/AllGenerics.R, R/plotting.R
+    Source: R/AllGenerics.R, R/plotting.R
     
     

 
@@ -57,7 +57,7 @@ 
Plotting a contact matrix

 
 montage(x, ...)
 
-# S4 method for HiCExperiment
+# S4 method for class 'HiCExperiment'
 plotMatrix(
   x,
   compare.to = NULL,
@@ -77,7 +77,7 @@ 
Plotting a contact matrix

   caption = TRUE
 )
 
-# S4 method for GInteractions
+# S4 method for class 'GInteractions'
 plotMatrix(
   x,
   use.scores = NULL,
@@ -95,7 +95,7 @@ 
Plotting a contact matrix

   cmap = NULL
 )
 
-# S4 method for matrix
+# S4 method for class 'matrix'
 plotMatrix(
   x,
   scale = "log10",
@@ -105,7 +105,7 @@ 
Plotting a contact matrix

   cmap = NULL
 )
 
-# S4 method for AggrHiCExperiment
+# S4 method for class 'AggrHiCExperiment'
 plotMatrix(
   x,
   use.scores = "balanced",
@@ -122,7 +122,7 @@ 
Plotting a contact matrix

   caption = TRUE
 )
 
-# S4 method for AggrHiCExperiment
+# S4 method for class 'AggrHiCExperiment'
 montage(
   x,
   use.scores = "balanced",
@@ -136,83 +136,83 @@ 
Plotting a contact matrix

 
     

     
Arguments

-    
x

+
+
+
x

 
A HiCExperiment object

 
 
-
...

+
...

 
Extra arguments passed to the corresponding method.

 
 
-
compare.to

+
compare.to

 
Compare to a second HiC matrix in the lower left corner

 
 
-
use.scores

+
use.scores

 
Which scores to use in the heatmap

 
 
-
scale

+
scale

 
Any of 'log10', 'log2', 'linear', 'exp0.2' (Default: 'log10')

 
 
-
maxDistance

+
maxDistance

 
maximum distance. If provided, the heatmap is plotted
 horizontally

 
 
-
loops

+
loops

 
Loops to plot on top of the heatmap, provided as GInteractions

 
 
-
borders

+
borders

 
Borders to plot on top of the heatmap, provided as GRanges

 
 
-
tracks

+
tracks

 
Named list of bigwig tracks imported as Rle

 
 
-
limits

+
limits

 
color map limits

 
 
-
dpi

+
dpi

 
DPI to create the plot (Default: 500)

 
 
-
rasterize

+
rasterize

 
Whether the generated heatmap is rasterized or vectorized
 (Default: TRUE)

 
 
-
symmetrical

+
symmetrical

 
Whether to enforce a symetrical heatmap (Default: TRUE)

 
 
-
chrom_lines

+
chrom_lines

 
Whether to display separating lines between chromosomes,
 should any be necessary (Default: TRUE)

 
 
-
show_grid

+
show_grid

 
Whether to display an underlying grid (Default: FALSE)

 
 
-
cmap

+
cmap

 
Color scale to use. (Default: bgrColors() if limits are c(-1, 1)
 and coolerColors() otherwise)

 
 
-
caption

+
caption

 
Whether to display a caption (Default: TRUE)

 
 

     

     
Value

-    
-
-
ggplot object

+    
ggplot object

     

 
     

@@ -241,15 +241,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/plotPs-1.png b/reference/plotPs-1.png
index fdf896d..1f5fd58 100644
Binary files a/reference/plotPs-1.png and b/reference/plotPs-1.png differ
diff --git a/reference/plotPs-2.png b/reference/plotPs-2.png
index cf7f548..0378ff5 100644
Binary files a/reference/plotPs-2.png and b/reference/plotPs-2.png differ
diff --git a/reference/plotPs-3.png b/reference/plotPs-3.png
index 1587a12..aa58d59 100644
Binary files a/reference/plotPs-3.png and b/reference/plotPs-3.png differ
diff --git a/reference/plotPs.html b/reference/plotPs.html
index 2687e2f..a1f4a60 100644
--- a/reference/plotPs.html
+++ b/reference/plotPs.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Plotting a P(s) distance law

-    Source: R/plotting.R
+    Source: R/plotting.R
     
     

 
@@ -60,27 +60,27 @@ 
Plotting a P(s) distance law

 
     

     
Arguments

-    
x

+
+
+
x

 
the output data.frame of distanceLaw function

 
 
-
mapping

+
mapping

 
aes to pass on to ggplot2

 
 
-
xlim

+
xlim

 
xlim

 
 
-
ylim

+
ylim

 
ylim

 
 

     

     
Value

-    
-
-
ggplot

+    
ggplot

     

 
     

@@ -134,15 +134,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/plotSaddle.html b/reference/plotSaddle.html
index 5df6361..7811c1c 100644
--- a/reference/plotSaddle.html
+++ b/reference/plotSaddle.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Plotting saddle plots

-    Source: R/plotting.R
+    Source: R/plotting.R
     
     

 
@@ -64,31 +64,31 @@ 
Plotting saddle plots

 
     

     
Arguments

-    
x

+
+
+
x

 
a HiCExperiment object with a stored eigens metadata

 
 
-
nbins

+
nbins

 
Number of bins to use to discretize the eigenvectors

 
 
-
limits

+
limits

 
limits for color map being used

 
 
-
plotBins

+
plotBins

 
Whether to plot the distribution of bins on top of the plot

 
 
-
BPPARAM

+
BPPARAM

 
a BiocParallel registered method

 
 

     

     
Value

-    
-
-
ggplot

+    
ggplot

     

 
   

@@ -103,15 +103,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/plotScalogram-1.png b/reference/plotScalogram-1.png
index b507688..784b119 100644
Binary files a/reference/plotScalogram-1.png and b/reference/plotScalogram-1.png differ
diff --git a/reference/plotScalogram.html b/reference/plotScalogram.html
index 833cdc6..72e0db1 100644
--- a/reference/plotScalogram.html
+++ b/reference/plotScalogram.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Plotting scalograms

-    Source: R/plotting.R
+    Source: R/plotting.R
     
     

 
@@ -58,19 +58,19 @@ 
Plotting scalograms

 
     

     
Arguments

-    
x

+
+
+
x

 
GRanges, the output of scalogram()

 
 
-
ylim

+
ylim

 
Range of distances to use for y-axis in scalograms

 
 

     

     
Value

-    
-
-
ggplot

+    
ggplot

     

 
     

@@ -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/11301f395da_7753 in memory. This may take a while...
+#> Importing pairs file /github/home/.cache/R/ExperimentHub/1c72216031c6_7753 in memory. This may take a while...
 plotScalogram(scalo)
 
 

@@ -101,15 +101,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/reexports.html b/reference/reexports.html
index 973c3a5..f498703 100644
--- a/reference/reexports.html
+++ b/reference/reexports.html
@@ -10,7 +10,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Objects exported from other packages

-    Source: R/reexports.R
+    Source: R/reexports.R
     
     

 
@@ -78,15 +78,15 @@ 
Objects exported from other packages

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/scalogram.html b/reference/scalogram.html
index 86ac5eb..c608d38 100644
--- a/reference/scalogram.html
+++ b/reference/scalogram.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Compute a scalogram of contacts

-    Source: R/scalogram.R
+    Source: R/scalogram.R
     
     

 
@@ -58,29 +58,27 @@ 
Compute a scalogram of contacts

 
     

     
Arguments

-    
x

+
+
+
x

 
A HiCExperiment object

 
 
-
dist_min

+
dist_min

 
Minimum distance for interactions to be considered.

 
 
-
nbins

+
nbins

 
Number of bins to divide each chromosome

 
 
-
probs

+
probs

 
Quantiles of interactions

 
 

     

     
Value

-    
-
-
a tibble

-
-
+    
a tibble

 
a tibble

     

 
@@ -95,7 +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/11301f395da_7753 in memory. This may take a while...
+#> Importing pairs file /github/home/.cache/R/ExperimentHub/1c72216031c6_7753 in memory. This may take a while...
 scalo
 #> # A tibble: 750 × 4
 #> # Groups:   chr, binned_pos [250]
@@ -126,15 +124,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/tracks.html b/reference/tracks.html
index 7561768..95c668f 100644
--- a/reference/tracks.html
+++ b/reference/tracks.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Aligning tracks with HiCExperiment objects

-    Source: R/tracks.R
+    Source: R/tracks.R
     
     

 
@@ -53,31 +53,29 @@ 
Aligning tracks with HiCExperiment objects

     

 
     

-    
# S4 method for HiCExperiment
+    
# S4 method for class 'HiCExperiment'
 coverage(x, use.pairs = FALSE, bin.size = resolution(x))

     

 
     

     
Arguments

-    
x

+
+
+
x

 
A HiCExperiment object over a full genome

 
 
-
use.pairs

+
use.pairs

 
logical. Whether to use pairsFile to compute Hi-C coverage

 
 
-
bin.size

+
bin.size

 
if use.pairs == TRUE, to which resolution

 
 

     

     
Value

-    
-
-
A HiCExperiment object with 2 added columns in regions(x)

-
-
+    
A HiCExperiment object with 2 added columns in regions(x)

     

 
     

@@ -129,15 +127,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/virtual4C.html b/reference/virtual4C.html
index b329936..823769f 100644
--- a/reference/virtual4C.html
+++ b/reference/virtual4C.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Computing virtual 4C profiles

-    Source: R/4C.R
+    Source: R/4C.R
     
     

 
@@ -60,23 +60,23 @@ 
Computing virtual 4C profiles

 
     

     
Arguments

-    
x

+
+
+
x

 
a HiCExperiment object

 
 
-
viewpoint

+
viewpoint

 
viewpoint, defined as a GRanges

 
 
-
use.scores

+
use.scores

 
use.scores

 
 

     

     
Value

-    
-
-
A tibble with the contact frequency of the viewpoint, per bin
+    
A tibble with the contact frequency of the viewpoint, per bin
 along the imported genomic range.

     

 
@@ -131,15 +131,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/sitemap.xml b/sitemap.xml
index 10d5e1c..04c784d 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -1,84 +1,30 @@
-
-
-  
-    /404.html
-  
-  
-    /LICENSE-text.html
-  
-  
-    /LICENSE.html
-  
-  
-    /articles/HiContacts.html
-  
-  
-    /articles/index.html
-  
-  
-    /authors.html
-  
-  
-    /index.html
-  
-  
-    /reference/Contacts.html
-  
-  
-    /reference/HiContacts-plots.html
-  
-  
-    /reference/Ps.html
-  
-  
-    /reference/arithmetics.html
-  
-  
-    /reference/checks.html
-  
-  
-    /reference/cisTransRatio.html
-  
-  
-    /reference/getCompartments.html
-  
-  
-    /reference/getDiamondInsulation.html
-  
-  
-    /reference/getLoops.html
-  
-  
-    /reference/index.html
-  
-  
-    /reference/palettes.html
-  
-  
-    /reference/plot4C.html
-  
-  
-    /reference/plotMatrix.html
-  
-  
-    /reference/plotPs.html
-  
-  
-    /reference/plotSaddle.html
-  
-  
-    /reference/plotScalogram.html
-  
-  
-    /reference/reexports.html
-  
-  
-    /reference/scalogram.html
-  
-  
-    /reference/tracks.html
-  
-  
-    /reference/virtual4C.html
-  
+
+/404.html
+/LICENSE-text.html
+/LICENSE.html
+/articles/HiContacts.html
+/articles/index.html
+/authors.html
+/index.html
+/reference/Contacts.html
+/reference/HiContacts-plots.html
+/reference/Ps.html
+/reference/arithmetics.html
+/reference/checks.html
+/reference/cisTransRatio.html
+/reference/getCompartments.html
+/reference/getDiamondInsulation.html
+/reference/getLoops.html
+/reference/index.html
+/reference/palettes.html
+/reference/plot4C.html
+/reference/plotMatrix.html
+/reference/plotPs.html
+/reference/plotSaddle.html
+/reference/plotScalogram.html
+/reference/reexports.html
+/reference/scalogram.html
+/reference/tracks.html
+/reference/virtual4C.html
 
+