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:
sample: yeast_wt, format = cool)sample: yeast_wt, format = mcool)sample: yeast_wt, format = pairs)sample: yeast_Eco1, format = mcool)sample: yeast_Eco1, format = pairs)sample: mESCs, format = mcool)sample: mESCs, format = pairs)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 notes
#> 1 yeast_wt cool S288C wild-type cool file @ resolution of 1kb
#> 2 yeast_wt mcool S288C wild-type multi-res mcool file
#> 3 yeast_wt pairs.gz S288C wild-type only pairs from chrII are provided
#> 4 yeast_eco1 mcool S288C Eco1-AID+IAA multi-res mcool file
#> 5 yeast_eco1 pairs.gz S288C Eco1-AID+IAA only pairs from chrII are provided
#> 6 mESCs mcool mm10 mESCs multi-res mcool file
#> 7 mESCs pairs.gz mm10 mESCs only pairs from chr13 are provided
#> EHID
#> 1 EH7701
#> 2 EH7702
#> 3 EH7703
#> 4 EH7704
#> 5 EH7705
#> 6 EH7706
#> 7 EH7707
#>
cool_file <- HiContactsData(sample = 'yeast_wt', format = 'cool')
#> snapshotDate(): 2022-10-24
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
cool_file
#> EH7701
#> "/home/biocbuild/.cache/R/ExperimentHub/3508b72098fa84_7751"HiContacts package can be used to import data provided by HiContactsData.
Refer to HiContacts package documentation for further information.
sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.5 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
#> LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
#>
#> 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
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] HiContactsData_1.0.0 ExperimentHub_2.6.0 AnnotationHub_3.6.0
#> [4] BiocFileCache_2.6.0 dbplyr_2.2.1 BiocGenerics_0.44.0
#> [7] BiocStyle_2.26.0
#>
#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.9 png_0.1-7
#> [3] Biostrings_2.66.0 assertthat_0.2.1
#> [5] digest_0.6.30 utf8_1.2.2
#> [7] mime_0.12 R6_2.5.1
#> [9] GenomeInfoDb_1.34.0 stats4_4.2.1
#> [11] RSQLite_2.2.18 evaluate_0.17
#> [13] httr_1.4.4 pillar_1.8.1
#> [15] zlibbioc_1.44.0 rlang_1.0.6
#> [17] curl_4.3.3 jquerylib_0.1.4
#> [19] blob_1.2.3 S4Vectors_0.36.0
#> [21] rmarkdown_2.17 stringr_1.4.1
#> [23] RCurl_1.98-1.9 bit_4.0.4
#> [25] shiny_1.7.3 compiler_4.2.1
#> [27] httpuv_1.6.6 xfun_0.34
#> [29] pkgconfig_2.0.3 htmltools_0.5.3
#> [31] tidyselect_1.2.0 KEGGREST_1.38.0
#> [33] GenomeInfoDbData_1.2.9 tibble_3.1.8
#> [35] interactiveDisplayBase_1.36.0 bookdown_0.29
#> [37] IRanges_2.32.0 fansi_1.0.3
#> [39] withr_2.5.0 crayon_1.5.2
#> [41] dplyr_1.0.10 later_1.3.0
#> [43] bitops_1.0-7 rappdirs_0.3.3
#> [45] jsonlite_1.8.3 xtable_1.8-4
#> [47] lifecycle_1.0.3 DBI_1.1.3
#> [49] magrittr_2.0.3 cli_3.4.1
#> [51] stringi_1.7.8 cachem_1.0.6
#> [53] XVector_0.38.0 promises_1.2.0.1
#> [55] bslib_0.4.0 ellipsis_0.3.2
#> [57] filelock_1.0.2 generics_0.1.3
#> [59] vctrs_0.5.0 tools_4.2.1
#> [61] bit64_4.0.5 Biobase_2.58.0
#> [63] glue_1.6.2 purrr_0.3.5
#> [65] BiocVersion_3.16.0 fastmap_1.1.0
#> [67] yaml_2.3.6 AnnotationDbi_1.60.0
#> [69] BiocManager_1.30.19 memoise_2.0.1
#> [71] knitr_1.40 sass_0.4.2