Fetches files from the DNAZoo data portal and caches them using the BiocFileCache system.
Arguments
- species
Any species processed by the DNA Zoo (check https://www.dnazoo.org/assemblies) for a browser-based explorer.
Value
DNAZooData() returns a HicFile object, which can then be
imported in memory using HiCExperiment::import().
Metadata also points to a URL to directly fetch the genome assembly
corrected by the DNA Zoo consortium.
Examples
###################################
## Importing DNAZoo `.hic` files ##
###################################
head(DNAZooData())
#> species readme
#> 1 Acinonyx_jubatus Acinonyx_jubatus/README.json
#> 2 Acropora_millepora Acropora_millepora/README.json
#> 3 Addax_nasomaculatus Addax_nasomaculatus/README.json
#> 4 Aedes_aegypti Aedes_aegypti/README.json
#> 5 Aedes_aegypti__AaegL4 Aedes_aegypti__AaegL4/README.json
#> 6 Aedes_aegypti__AaegL5.0 Aedes_aegypti__AaegL5.0/README.json
#> readme_link
#> 1 https://dnazoo.s3.wasabisys.com/Acinonyx_jubatus/README.json
#> 2 https://dnazoo.s3.wasabisys.com/Acropora_millepora/README.json
#> 3 https://dnazoo.s3.wasabisys.com/Addax_nasomaculatus/README.json
#> 4 https://dnazoo.s3.wasabisys.com/Aedes_aegypti/README.json
#> 5 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL4/README.json
#> 6 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL5.0/README.json
#> original_assembly new_assembly
#> 1 aciJub1 aciJub1_HiC
#> 2 amil_sf_1.1 amil_sf_1.1_HiC
#> 3 ASM1959352v1 ASM1959352v1_HiC
#> 4 AGWG.draft AaegL5.0
#> 5 AaegL3 AaegL4
#> 6 AGWG.draft AaegL5.0
#> new_assembly_link
#> 1 https://dnazoo.s3.wasabisys.com/Acinonyx_jubatus/aciJub1_HiC.fasta.gz
#> 2 https://dnazoo.s3.wasabisys.com/Acropora_millepora/amil_sf_1.1_HiC.fasta.gz
#> 3 https://dnazoo.s3.wasabisys.com/Addax_nasomaculatus/ASM1959352v1_HiC.fasta.gz
#> 4 https://dnazoo.s3.wasabisys.com/Aedes_aegypti/AaegL5.0.fasta.gz
#> 5 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL4/AaegL4.fasta.gz
#> 6 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL5.0/AaegL5.0.fasta.gz
#> new_assembly_link_status
#> 1 200
#> 2 200
#> 3 200
#> 4 404
#> 5 200
#> 6 200
#> hic_link
#> 1 https://dnazoo.s3.wasabisys.com/Acinonyx_jubatus/aciJub1.rawchrom.hic
#> 2 https://dnazoo.s3.wasabisys.com/Acropora_millepora/amil_sf_1.1_HiC.hic
#> 3 https://dnazoo.s3.wasabisys.com/Addax_nasomaculatus/ASM1959352v1_HiC.hic
#> 4 <NA>
#> 5 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL4/AaegL4.hic
#> 6 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL5.0/AaegL5.0.hic
hf <- DNAZooData(species = 'Anolis_carolinensis')
hf
#> HicFile object
#> .hic file: /github/home/.cache/R/DNAZooData/665c5fbf1694_AnoCar2.0_HiC.hic
#> resolution: 5000
#> pairs file:
#> metadata(6): organism draftAssembly ... credits assemblyURL