Contents

0.1 Introduction to HiContactsData

HiContactsData is a companion data package giving programmatic access to several processed Hi-C files for demonstration, such as cool, mcool and pairs files. It is meant to be used with HiContacts.

library(HiContactsData)

The only function provided by HiContactsData package is HiContactsData(). Several files are avaible using this function, namely:

Yeast data comes from Bastie, Chapard et al., Nature Structural & Molecular Biology 2022 and mouse ESC data comes from Bonev et al., Cell 2017.

To download one of these files, one can specify a sample and a file format:

cool_file <- HiContactsData()
#> Available files:
#>        sample        format genome    condition
#> 1    yeast_wt      fastq_R1  S288C    wild-type
#> 2    yeast_wt      fastq_R2  S288C    wild-type
#> 3    yeast_wt    HiCool_log  S288C    wild-type
#> 4    yeast_wt      pairs.gz  S288C    wild-type
#> 5    yeast_wt          cool  S288C    wild-type
#> 6    yeast_wt         mcool  S288C    wild-type
#> 7    yeast_wt           hic  S288C    wild-type
#> 8    yeast_wt hicpro_matrix  S288C    wild-type
#> 9    yeast_wt    hicpro_bed  S288C    wild-type
#> 10   yeast_wt  hicpro_pairs  S288C    wild-type
#> 11 yeast_eco1         mcool  S288C Eco1-AID+IAA
#> 12 yeast_eco1      pairs.gz  S288C Eco1-AID+IAA
#> 13      mESCs         mcool   mm10        mESCs
#> 14      mESCs      pairs.gz   mm10        mESCs
#>                                 notes   EHID
#> 1                          fastq (R1) EH7783
#> 2                          fastq (R2) EH7784
#> 3                     HiCool log file EH7785
#> 4  only pairs from chrII are provided EH7703
#> 5      .cool file @ resolution of 1kb EH7701
#> 6               multi-res .mcool file EH7702
#> 7                 multi-res .hic file EH7786
#> 8           HiC-Pro matrix file @ 1kb EH7787
#> 9              HiC-Pro bed file @ 1kb EH7788
#> 10        HiC-Pro .allValidPairs file EH7789
#> 11              multi-res .mcool file EH7704
#> 12 only pairs from chrII are provided EH7705
#> 13              multi-res .mcool file EH7706
#> 14 only pairs from chr13 are provided EH7707
#> 
cool_file <- HiContactsData(sample = 'yeast_wt', format = 'cool')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
cool_file
#>                                                       EH7701 
#> "/home/biocbuild/.cache/R/ExperimentHub/27bf6a6af11c1f_7751"

0.2 HiContacts and HiContactsData

HiCExperiment package can be used to import data provided by HiContactsData. Refer to HiCExperiment package documentation for further information.

0.3 Session info

sessionInfo()
#> R version 4.3.1 (2023-06-16)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.3 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: America/New_York
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] HiContactsData_1.4.0 ExperimentHub_2.10.0 AnnotationHub_3.10.0
#> [4] BiocFileCache_2.10.0 dbplyr_2.3.4         BiocGenerics_0.48.0 
#> [7] BiocStyle_2.30.0    
#> 
#> loaded via a namespace (and not attached):
#>  [1] KEGGREST_1.42.0               xfun_0.40                    
#>  [3] bslib_0.5.1                   Biobase_2.62.0               
#>  [5] bitops_1.0-7                  vctrs_0.6.4                  
#>  [7] tools_4.3.1                   generics_0.1.3               
#>  [9] stats4_4.3.1                  curl_5.1.0                   
#> [11] tibble_3.2.1                  fansi_1.0.5                  
#> [13] AnnotationDbi_1.64.0          RSQLite_2.3.1                
#> [15] blob_1.2.4                    pkgconfig_2.0.3              
#> [17] S4Vectors_0.40.0              GenomeInfoDbData_1.2.11      
#> [19] lifecycle_1.0.3               compiler_4.3.1               
#> [21] Biostrings_2.70.1             GenomeInfoDb_1.38.0          
#> [23] httpuv_1.6.12                 htmltools_0.5.6.1            
#> [25] sass_0.4.7                    RCurl_1.98-1.12              
#> [27] yaml_2.3.7                    interactiveDisplayBase_1.40.0
#> [29] pillar_1.9.0                  later_1.3.1                  
#> [31] crayon_1.5.2                  jquerylib_0.1.4              
#> [33] ellipsis_0.3.2                cachem_1.0.8                 
#> [35] mime_0.12                     tidyselect_1.2.0             
#> [37] digest_0.6.33                 purrr_1.0.2                  
#> [39] dplyr_1.1.3                   bookdown_0.36                
#> [41] BiocVersion_3.18.0            fastmap_1.1.1                
#> [43] cli_3.6.1                     magrittr_2.0.3               
#> [45] utf8_1.2.4                    withr_2.5.1                  
#> [47] filelock_1.0.2                promises_1.2.1               
#> [49] rappdirs_0.3.3                bit64_4.0.5                  
#> [51] rmarkdown_2.25                XVector_0.42.0               
#> [53] httr_1.4.7                    bit_4.0.5                    
#> [55] png_0.1-8                     memoise_2.0.1                
#> [57] shiny_1.7.5.1                 evaluate_0.22                
#> [59] knitr_1.44                    IRanges_2.36.0               
#> [61] rlang_1.1.1                   Rcpp_1.0.11                  
#> [63] xtable_1.8-4                  glue_1.6.2                   
#> [65] DBI_1.1.3                     BiocManager_1.30.22          
#> [67] jsonlite_1.8.7                R6_2.5.1                     
#> [69] zlibbioc_1.48.0