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Author: bschilder

articles/cell_type_specific_epigenomics.html

@@ -18,17 +18,16 @@ library(echoannot)
 
 #### Import data
 
+*Note:* These functions download remote bigwig files from UCSC, which
+requires network access and may take several minutes.
+
 ``` r
 
 superenhancers <- echoannot::get_NOTT2019_superenhancer_interactome()
 enhancers_promoters <- echoannot::NOTT2019_get_promoter_interactome_data()
 peaks <- echoannot::NOTT2019_get_epigenomic_peaks()
 ```
 
-    ## Importing previously downloaded files: /github/home/.cache/R/echoannot/NOTT2019_epigenomic_peaks.rds
-
-    ## ++ NOTT2019:: 634,540 ranges retrieved.
-
 #### Plot
 
 ``` r
@@ -37,97 +36,19 @@ dat <- echodata::BST1
 histo_out <- echoannot::NOTT2019_epigenomic_histograms(dat = dat)
 ```
 
-    ## NOTT2019:: Creating epigenomic histograms plot
-
-    ## + Inferring genomic limits for window: 1x
-
-    ## Constructing GRanges query using min/max ranges across one or more chromosomes.
-
-    ## Downloading data from UCSC.
-
-    ## Importing... [1] exvivo_H3K27ac_tbp
-
-    ## Importing... [2] microglia_H3K27ac
-
-    ## Importing... [3] neurons_H3K27ac
-
-    ## Importing... [4] oligodendrocytes_H3K27ac
-
-    ## Importing... [5] astrocytes_H3K27ac
-
-    ## Importing... [6] exvivo_atac_tbp
-
-    ## Importing... [7] microglia_atac
-
-    ## Importing... [8] neurons_atac
-
-    ## Importing... [9] oligodendrocytes_atac
-
-    ## Importing... [10] astrocytes_atac
-
-    ## Importing... [11] microglia_H3K4me3
-
-    ## Importing... [12] neurons_H3K4me3
-
-    ## Importing... [13] oligodendrocytes_H3K4me3
-
-    ## Importing... [14] astrocytes_H3K4me3
-
-    ## Importing previously downloaded files: /github/home/.cache/R/echoannot/NOTT2019_epigenomic_peaks.rds
-
-    ## ++ NOTT2019:: 634,540 ranges retrieved.
-
-    ## dat is already a GRanges object.
-
-    ## 543 query SNP(s) detected with reference overlap.
-
-    ## + Calculating max histogram height
-
-    ## + Converting label units to Mb.
-
-    ## using coord:genome to parse x scale
-    ## using coord:genome to parse x scale
-
-    ## Warning in !vapply(ggl, fixed, logical(1L)) & !vapply(PlotList, is, "Ideogram",
-    ## : longer object length is not a multiple of shorter object length
-
-![](cell_type_specific_epigenomics_files/figure-html/nott2019_plot-1.png)
-
 In addition to the plot object, tables of both raw read ranges and
 called peaks are included in the output list.
 
 ``` r
 
 knitr::kable(head(histo_out$data$raw))
-```
-
-| seqnames | start | end | width | strand | score | Cell_type | Assay | Experiment |
-|:---|---:|---:|---:|:---|---:|:---|:---|:---|
-| chr4 | 14737349 | 14737411 | 63 | \* | 0.6 | microglia | H3K27ac | exvivo H3K27ac tbp |
-| chr4 | 14737488 | 14737562 | 75 | \* | 0.2 | microglia | H3K27ac | exvivo H3K27ac tbp |
-| chr4 | 14737692 | 14737766 | 75 | \* | 0.6 | microglia | H3K27ac | exvivo H3K27ac tbp |
-| chr4 | 14737782 | 14737856 | 75 | \* | 0.4 | microglia | H3K27ac | exvivo H3K27ac tbp |
-| chr4 | 14738054 | 14738126 | 73 | \* | 0.6 | microglia | H3K27ac | exvivo H3K27ac tbp |
-| chr4 | 14738127 | 14738128 | 2 | \* | 1.2 | microglia | H3K27ac | exvivo H3K27ac tbp |
-
-``` r
-
 knitr::kable(head(histo_out$data$peaks))
 ```
 
-| seqnames | start | end | width | strand | Assay | Marker | Cell_type | Cell_type.1 | Assay.1 | Experiment | y |
-|:---|---:|---:|---:|:---|:---|:---|:---|:---|:---|:---|---:|
-| 4 | 14745668 | 14746002 | 335 | \* | peaks | Olig2 | oligo | microglia | H3K27ac | exvivo H3K27ac tbp | -1.1e-06 |
-| 4 | 14751439 | 14751837 | 399 | \* | peaks | Olig2 | oligo | microglia | H3K27ac | exvivo H3K27ac tbp | -1.1e-06 |
-| 4 | 14768551 | 14768735 | 185 | \* | peaks | PU1 | microglia | microglia | H3K27ac | exvivo H3K27ac tbp | -1.1e-06 |
-| 4 | 14768704 | 14769257 | 554 | \* | peaks | PU1 | microglia | microglia | H3K27ac | exvivo H3K27ac tbp | -1.1e-06 |
-| 4 | 14771450 | 14773099 | 1650 | \* | peaks | LHX2 | astrocytes | microglia | H3K27ac | exvivo H3K27ac tbp | -1.1e-06 |
-| 4 | 14829018 | 14829146 | 129 | \* | peaks | NeuN | neurons | microglia | H3K27ac | exvivo H3K27ac tbp | -1.1e-06 |
-
 ### Corces2020
 
 `echoannot` also includes data generated by
-[“Corces2019”](https://doi.org/10.1038/s41588-020-00721-x):
+[“Corces2020”](https://doi.org/10.1038/s41588-020-00721-x):
 
 > Corces, M.R., Shcherbina, A., Kundu, S. et al. Single-cell epigenomic
 > analyses implicate candidate causal variants at inherited risk loci
@@ -147,10 +68,6 @@ scATACseq_peaks <- echoannot::get_CORCES2020_scATACseq_peaks()
 
 #### Plot
 
-*Note:* This chunk is kept as `eval=FALSE` because it depends on the
-`dat` variable from a prior analysis and
-[`ggbio::autoplot`](https://ggplot2.tidyverse.org/reference/autoplot.html).
-
 ``` r
 
 peak_dat <- echoannot::granges_overlap(
@@ -172,7 +89,7 @@ ggbio::autoplot(peak_dat,
 utils::sessionInfo()
 ```
 
-    ## R Under development (unstable) (2026-03-12 r89607)
+    ## R Under development (unstable) (2026-03-15 r89629)
     ## Platform: x86_64-pc-linux-gnu
     ## Running under: Ubuntu 24.04.4 LTS
     ## 
@@ -253,7 +170,7 @@ utils::sessionInfo()
     ## [105] bookdown_0.46               RBGL_1.87.0                
     ## [107] ProtGenerics_1.43.0         scales_1.4.0               
     ## [109] Biobase_2.71.0              lmom_3.2                   
-    ## [111] png_0.1-9                   knitr_1.51                 
+    ## [111] png_0.1-8                   knitr_1.51                 
     ## [113] rstudioapi_0.18.0           tzdb_0.5.0                 
     ## [115] reshape2_1.4.5              rjson_0.2.23               
     ## [117] checkmate_2.3.4             curl_7.0.0                 
@@ -265,19 +182,18 @@ utils::sessionInfo()
     ## [129] grid_4.6.0                  vctrs_0.7.1                
     ## [131] cluster_2.1.8.2             htmlTable_2.4.3            
     ## [133] evaluate_1.0.5              readr_2.2.0                
-    ## [135] GenomicFeatures_1.63.1      mvtnorm_1.3-6              
+    ## [135] GenomicFeatures_1.63.1      mvtnorm_1.3-5              
     ## [137] cli_3.6.5                   compiler_4.6.0             
     ## [139] Rsamtools_2.27.1            rlang_1.1.7                
-    ## [141] crayon_1.5.3                labeling_0.4.3             
-    ## [143] aws.signature_0.6.0         plyr_1.8.9                 
-    ## [145] forcats_1.0.1               fs_1.6.7                   
-    ## [147] stringi_1.8.7               viridisLite_0.4.3          
-    ## [149] BiocParallel_1.45.0         Biostrings_2.79.5          
-    ## [151] lazyeval_0.2.2              Matrix_1.7-4               
-    ## [153] downloadR_1.0.0             dir.expiry_1.19.0          
-    ## [155] BSgenome_1.79.1             patchwork_1.3.2            
-    ## [157] hms_1.1.4                   bit64_4.6.0-1              
-    ## [159] ggplot2_4.0.2               KEGGREST_1.51.1            
-    ## [161] SummarizedExperiment_1.41.1 haven_2.5.5                
-    ## [163] memoise_2.0.1               bslib_0.10.0               
-    ## [165] bit_4.6.0                   readxl_1.4.5
+    ## [141] crayon_1.5.3                aws.signature_0.6.0        
+    ## [143] plyr_1.8.9                  forcats_1.0.1              
+    ## [145] fs_1.6.7                    stringi_1.8.7              
+    ## [147] BiocParallel_1.45.0         Biostrings_2.79.5          
+    ## [149] lazyeval_0.2.2              Matrix_1.7-4               
+    ## [151] downloadR_1.0.0             dir.expiry_1.19.0          
+    ## [153] BSgenome_1.79.1             patchwork_1.3.2            
+    ## [155] hms_1.1.4                   bit64_4.6.0-1              
+    ## [157] ggplot2_4.0.2               KEGGREST_1.51.1            
+    ## [159] SummarizedExperiment_1.41.1 haven_2.5.5                
+    ## [161] memoise_2.0.1               bslib_0.10.0               
+    ## [163] bit_4.6.0                   readxl_1.4.5