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.
The only function provided by HiContactsData package is
HiContactsData(). Several files are available using this
function, namely:
- S288C fastq files (R1 & R2) (
sample:yeast_wt,format=fastq_R{12}) - S288C HiCool processing log (
sample:yeast_wt,format=HiCool_log) - S288C.cool (
sample:yeast_wt,format=cool) - S288C.mcool (
sample:yeast_wt,format=mcool) - S288C_G1.mcool (
sample:yeast_g1,format=mcool) - S288C_G2M.mcool (
sample:yeast_g1,format=mcool) - S288C_G1.pairs (
sample:yeast_g2m,format=pairs) - S288C_G2M.pairs (
sample:yeast_g2m,format=pairs) - S288C.hic (
sample:yeast_wt,format=hic) - S288C.hicpro.matrix (
sample:yeast_wt,format=hicpro_matrix) - S288C.hicpro.bed (
sample:yeast_wt,format=hicpro_bed) - S288C.pairs.gz for chrII only (
sample:yeast_wt,format=pairs) - S288C_Eco1-AID.mcool (
sample:yeast_Eco1,format=mcool) - S288C_Eco1-AID.pairs.gz for chrII only (
sample:yeast_Eco1,format=pairs) - mESCs.mcool (
sample:mESCs,format=mcool) - mESCs.pairs.gz for chr13 only (
sample:mESCs,format=pairs) - microC_HFFc6_chr17.mcool (
sample:microC,format=mcool)
Yeast data comes from Bastie, Chapard et al., Nature Structural & Molecular Biology 2022 and mouse ESC data comes from Bonev et al., Cell 2017. Human HcFF6 micro-C data comes from Krietenstein et al., Mol. Cell 2020.
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_g1 mcool S288C wild-type
#> 8 yeast_g1 pairs S288C wild-type
#> 9 yeast_g2m mcool S288C wild-type
#> 10 yeast_g2m pairs S288C wild-type
#> 11 yeast_wt hic S288C wild-type
#> 12 yeast_wt hicpro_matrix S288C wild-type
#> 13 yeast_wt hicpro_bed S288C wild-type
#> 14 yeast_wt hicpro_pairs S288C wild-type
#> 15 yeast_eco1 mcool S288C Eco1-AID+IAA
#> 16 yeast_eco1 pairs.gz S288C Eco1-AID+IAA
#> 17 mESCs mcool mm10 mESCs
#> 18 mESCs pairs.gz mm10 mESCs
#> 19 microC mcool GRCh38 HFFc6
#> 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 .mcool file EH8562
#> 8 filtered pairs are provided EH8564
#> 9 multi-res .mcool file EH8563
#> 10 filtered pairs are provided EH8565
#> 11 multi-res .hic file EH7786
#> 12 HiC-Pro matrix file @ 1kb EH7787
#> 13 HiC-Pro bed file @ 1kb EH7788
#> 14 HiC-Pro .allValidPairs file EH7789
#> 15 multi-res .mcool file EH7704
#> 16 only pairs from chrII are provided EH7705
#> 17 multi-res .mcool file EH7706
#> 18 only pairs from chr13 are provided EH7707
#> 19 multi-res .mcool file, only chr17 is provided EH8535
#>
cool_file <- HiContactsData(sample = 'yeast_wt', format = 'cool')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
cool_file
#> EH7701
#> "/github/home/.cache/R/ExperimentHub/1ba73bc4fbc4_7751"HiContacts and HiContactsData
HiCExperiment package can be used to import data
provided by HiContactsData. Refer to
HiCExperiment package documentation for further
information.
Session info
sessionInfo()
#> R Under development (unstable) (2024-01-09 r85796)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.3 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/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [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: UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] HiContactsData_1.5.3 ExperimentHub_2.11.1 AnnotationHub_3.11.1
#> [4] BiocFileCache_2.11.1 dbplyr_2.4.0 BiocGenerics_0.49.1
#> [7] BiocStyle_2.31.0
#>
#> loaded via a namespace (and not attached):
#> [1] KEGGREST_1.43.0 xfun_0.41 bslib_0.6.1
#> [4] Biobase_2.63.0 bitops_1.0-7 vctrs_0.6.5
#> [7] tools_4.4.0 generics_0.1.3 stats4_4.4.0
#> [10] curl_5.2.0 tibble_3.2.1 fansi_1.0.6
#> [13] AnnotationDbi_1.65.2 RSQLite_2.3.4 blob_1.2.4
#> [16] pkgconfig_2.0.3 desc_1.4.3 S4Vectors_0.41.3
#> [19] GenomeInfoDbData_1.2.11 lifecycle_1.0.4 compiler_4.4.0
#> [22] stringr_1.5.1 textshaping_0.3.7 Biostrings_2.71.1
#> [25] GenomeInfoDb_1.39.5 htmltools_0.5.7 sass_0.4.8
#> [28] RCurl_1.98-1.14 yaml_2.3.8 pillar_1.9.0
#> [31] pkgdown_2.0.7.9000 crayon_1.5.2 jquerylib_0.1.4
#> [34] cachem_1.0.8 mime_0.12 tidyselect_1.2.0
#> [37] digest_0.6.34 stringi_1.8.3 dplyr_1.1.4
#> [40] purrr_1.0.2 bookdown_0.37 BiocVersion_3.19.1
#> [43] fastmap_1.1.1 cli_3.6.2 magrittr_2.0.3
#> [46] utf8_1.2.4 withr_3.0.0 filelock_1.0.3
#> [49] rappdirs_0.3.3 bit64_4.0.5 rmarkdown_2.25
#> [52] XVector_0.43.1 httr_1.4.7 bit_4.0.5
#> [55] ragg_1.2.7 png_0.1-8 memoise_2.0.1
#> [58] evaluate_0.23 knitr_1.45 IRanges_2.37.0
#> [61] rlang_1.1.3 glue_1.7.0 DBI_1.2.1
#> [64] BiocManager_1.30.22 jsonlite_1.8.8 R6_2.5.1
#> [67] systemfonts_1.0.5 fs_1.6.3 zlibbioc_1.49.0