Last updated: 2021-04-13

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Knit directory: hesc-epigenomics/

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File Version Author Date Message
Rmd 6e3bb86 cnluzon 2021-04-13 wflow_publish(“./analysis/bivalent_chromatin.Rmd”)
html 0481b52 cnluzon 2021-02-05 RNA seq first analysis
html 87ff15f cnluzon 2021-02-05 Renamed read counts file
html 8445aca cnluzon 2021-02-03 Build site.
Rmd 70a54dd cnluzon 2021-02-03 Bivalent chromatin profiles

Summary

This is a study on bivalent chromatin regions.

As a base annotation we use the bivalent regions annotated in Court 2017:

Court, Franck, and Philippe Arnaud. “An annotated list of bivalent chromatin regions in human ES cells: a new tool for cancer epigenetic research.” Oncotarget 8.3 (2017): 4110.

Additionally, the bivalent genes annotated as such in their supplementary file 1: https://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=downloadSuppFile&path%5B%5D=13746&path%5B%5D=21048

Bivalent regions file: Original regions were translated to hg38 with liftOver: data/bed/Bivalent_Court2017.hg38.bed.

colors_list <- c("Naive_EZH2i"="#5F9EA0",
                 "Naive_Untreated"="#278b8b",
                 "Primed_EZH2i"="#f47770",
                 "Primed_Untreated"="#f44b34")

style_info <- read.table(params$styles, header = T, sep = "\t")
rownames(style_info) <- style_info$bw

Bivalent regions

biv_ranges <- import(params$biv, )
biv_ranges
GRanges object with 5763 ranges and 0 metadata columns:
         seqnames            ranges strand
            <Rle>         <IRanges>  <Rle>
     [1]     chr1     922893-927228      *
     [2]     chr1     938978-943553      *
     [3]     chr1     958524-962043      *
     [4]     chr1     965864-967597      *
     [5]     chr1    997897-1002325      *
     ...      ...               ...    ...
  [5759]    chr22 50269325-50272471      *
  [5760]    chr22 50305876-50307401      *
  [5761]    chr22 50529375-50532912      *
  [5762]    chr22 50672502-50674162      *
  [5763]    chr22 50696573-50698241      *
  -------
  seqinfo: 22 sequences from an unspecified genome; no seqlengths

H3K4m3

bwfiles <- list.files(file.path(params$datadir, "bw/Kumar_2020/"), full.names = T)

bwinput <- bwfiles[grepl("IN.*pooled", bwfiles)]
bwfiles <- bwfiles[grepl("H3K4m3.*pooled.hg38.scaled", bwfiles)]

colors <- as.character(style_info[basename(c(bwfiles, bwinput)), "color_cond"])
labels <- style_info[basename(c(bwfiles, bwinput)), "label"]

plot_bw_profile(
  c(bwfiles, bwinput),
  params$biv,
  mode = "center",
  upstream = 10000,
  downstream = 10000,
  colors = colors,
  labels = labels
) + ggtitle("H3K4m3 at bivalent regions")

Version Author Date
0481b52 cnluzon 2021-02-05
87ff15f cnluzon 2021-02-05
8445aca cnluzon 2021-02-03

Norm to input:

bwfiles <- list.files(file.path(params$datadir, "bw/Kumar_2020/"), full.names = T)

bwinput <- bwfiles[grepl("IN.*pooled", bwfiles)]
bwfiles <- bwfiles[grepl("H3K4m3.*pooled.hg38.scaled", bwfiles)]

colors <- as.character(style_info[basename(bwfiles), "color_cond"])
labels <- style_info[basename(bwfiles), "label"]

plot_bw_profile(
  bwfiles,
  bg_bwfiles = bwinput,
  params$biv,
  mode = "center",
  upstream = 10000,
  downstream = 10000,
  colors = colors,
  labels = labels
) + ggtitle("H3K4m3 at bivalent regions")

Version Author Date
0481b52 cnluzon 2021-02-05
87ff15f cnluzon 2021-02-05
8445aca cnluzon 2021-02-03

H3K27m3

bwfiles <- list.files(file.path(params$datadir, "bw/Kumar_2020/"), full.names = T)

bwinput <- bwfiles[grepl("IN.*pooled", bwfiles)]
bwfiles <- bwfiles[grepl("H3K27m3.*pooled.hg38.scaled", bwfiles)]

colors <- as.character(style_info[basename(c(bwfiles, bwinput)), "color_cond"])
labels <- style_info[basename(c(bwfiles, bwinput)), "label"]

plot_bw_profile(
  c(bwfiles, bwinput),
  params$biv,
  mode = "center",
  upstream = 10000,
  downstream = 10000,
  colors = colors,
  labels = labels
) + ggtitle("H3K27m3 at bivalent regions")

Version Author Date
0481b52 cnluzon 2021-02-05
87ff15f cnluzon 2021-02-05
8445aca cnluzon 2021-02-03

Norm to input:

bwfiles <- list.files(file.path(params$datadir, "bw/Kumar_2020/"), full.names = T)

bwinput <- bwfiles[grepl("IN.*pooled", bwfiles)]
bwfiles <- bwfiles[grepl("H3K27m3.*pooled.hg38.scaled", bwfiles)]

colors <- as.character(style_info[basename(bwfiles), "color_cond"])
labels <- style_info[basename(bwfiles), "label"]

plot_bw_profile(
  bwfiles, 
  bg_bwfiles = bwinput,
  params$biv,
  mode = "center",
  upstream = 10000,
  downstream = 10000,
  colors = colors,
  labels = labels,
  bin_size = 200
) + ggtitle("H3K27m3 at bivalent regions")

Version Author Date
0481b52 cnluzon 2021-02-05
87ff15f cnluzon 2021-02-05
8445aca cnluzon 2021-02-03

H2AUb

bwfiles <- list.files(file.path(params$datadir, "bw/Kumar_2020/"), full.names = T)

bwinput <- bwfiles[grepl("IN.*pooled", bwfiles)]
bwfiles <- bwfiles[grepl("H2A.*pooled.hg38.scaled", bwfiles)]

colors <- as.character(style_info[basename(c(bwfiles, bwinput)), "color_cond"])
labels <- style_info[basename(c(bwfiles, bwinput)), "label"]

plot_bw_profile(
  c(bwfiles, bwinput),
  params$biv,
  mode = "center",
  upstream = 10000,
  downstream = 10000,
  colors = colors,
  labels = labels
) + ggtitle("H2Aub at bivalent regions")

Version Author Date
0481b52 cnluzon 2021-02-05
87ff15f cnluzon 2021-02-05
8445aca cnluzon 2021-02-03

Norm to input:

bwfiles <- list.files(file.path(params$datadir, "bw/Kumar_2020/"), full.names = T)

bwinput <- bwfiles[grepl("IN.*pooled", bwfiles)]
bwfiles <- bwfiles[grepl("H2A.*pooled.hg38.scaled", bwfiles)]

colors <- as.character(style_info[basename(bwfiles), "color_cond"])
labels <- style_info[basename(bwfiles), "label"]

plot_bw_profile(
  bwfiles, 
  bg_bwfiles = bwinput,
  params$biv,
  mode = "center",
  upstream = 10000,
  downstream = 10000,
  colors = colors,
  labels = labels,
  bin_size = 200
) + ggtitle("H2Aub at bivalent regions")

Version Author Date
0481b52 cnluzon 2021-02-05
87ff15f cnluzon 2021-02-05
8445aca cnluzon 2021-02-03

sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=sv_SE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=sv_SE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=sv_SE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=sv_SE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] svglite_2.0.0                           
 [2] purrr_0.3.4                             
 [3] ggplot2_3.3.3                           
 [4] rtracklayer_1.50.0                      
 [5] org.Hs.eg.db_3.11.4                     
 [6] TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0
 [7] GenomicFeatures_1.40.1                  
 [8] AnnotationDbi_1.52.0                    
 [9] Biobase_2.50.0                          
[10] GenomicRanges_1.42.0                    
[11] GenomeInfoDb_1.26.2                     
[12] IRanges_2.24.1                          
[13] S4Vectors_0.28.1                        
[14] BiocGenerics_0.36.0                     
[15] wigglescout_0.12.8                      
[16] workflowr_1.6.2                         

loaded via a namespace (and not attached):
 [1] bitops_1.0-6                matrixStats_0.58.0         
 [3] fs_1.5.0                    bit64_4.0.5                
 [5] RColorBrewer_1.1-2          progress_1.2.2             
 [7] httr_1.4.2                  rprojroot_2.0.2            
 [9] tools_4.0.5                 R6_2.5.0                   
[11] DBI_1.1.1                   colorspace_2.0-0           
[13] withr_2.4.1                 tidyselect_1.1.0           
[15] prettyunits_1.1.1           curl_4.3                   
[17] bit_4.0.4                   compiler_4.0.5             
[19] git2r_0.28.0                xml2_1.3.2                 
[21] DelayedArray_0.16.0         labeling_0.4.2             
[23] scales_1.1.1                askpass_1.1                
[25] rappdirs_0.3.3              systemfonts_1.0.1          
[27] stringr_1.4.0               digest_0.6.27              
[29] Rsamtools_2.6.0             rmarkdown_2.6              
[31] XVector_0.30.0              pkgconfig_2.0.3            
[33] htmltools_0.5.1.1           parallelly_1.23.0          
[35] MatrixGenerics_1.2.0        highr_0.8                  
[37] dbplyr_2.1.0                fastmap_1.1.0              
[39] rlang_0.4.10                RSQLite_2.2.3              
[41] farver_2.0.3                generics_0.1.0             
[43] BiocParallel_1.24.1         dplyr_1.0.4                
[45] RCurl_1.98-1.2              magrittr_2.0.1             
[47] GenomeInfoDbData_1.2.4      Matrix_1.3-2               
[49] Rcpp_1.0.6                  munsell_0.5.0              
[51] lifecycle_1.0.0             furrr_0.2.2                
[53] stringi_1.5.3               whisker_0.4                
[55] yaml_2.2.1                  SummarizedExperiment_1.20.0
[57] zlibbioc_1.36.0             plyr_1.8.6                 
[59] BiocFileCache_1.12.1        grid_4.0.5                 
[61] blob_1.2.1                  listenv_0.8.0              
[63] promises_1.2.0.1            crayon_1.4.1               
[65] lattice_0.20-41             Biostrings_2.58.0          
[67] hms_1.0.0                   knitr_1.31                 
[69] pillar_1.4.7                reshape2_1.4.4             
[71] codetools_0.2-18            biomaRt_2.44.4             
[73] XML_3.99-0.5                glue_1.4.2                 
[75] evaluate_0.14               vctrs_0.3.6                
[77] httpuv_1.5.5                gtable_0.3.0               
[79] openssl_1.4.3               future_1.21.0              
[81] assertthat_0.2.1            cachem_1.0.4               
[83] xfun_0.21                   later_1.1.0.1              
[85] tibble_3.0.6                GenomicAlignments_1.26.0   
[87] memoise_2.0.0               globals_0.14.0             
[89] ellipsis_0.3.1