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The PR2 database is provided as a data frame.

This is a join between the following tables:

  • pr2_main

  • pr2_taxonomy

  • pr2_sequence

  • pr2_metadata

  • pr2_traits

  • pr2_silva

  • euribo

The metadata contains different types of fields

  • gb_ : originating from the GenBank entry

  • eukref_ : annotated by the Eukref project

  • pr2_ : annotated by pr2 such latitude and longitude

  • eukribo_: information from the EukRibo database

Description of fields: https://pr2-database.org/documentation/pr2-fields

Usage

pr2_database()

Value

A data frame

Examples


# Read the whole database
my_pr2 <- pr2_database()

# Select a specific genus
pr2_ostreo <- pr2_database()
pr2_ostreo <- dplyr::filter(pr2_ostreo , genus == "Ostreococcus")
pr2_ostreo <-  dplyr::select(pr2_ostreo, pr2_accession, species)
head(pr2_ostreo)
#> # A tibble: 6 × 2
#>   pr2_accession     species                   
#>   <chr>             <chr>                     
#> 1 AF525872.1.1766_U Ostreococcus_lucimarinus  
#> 2 EU562149.1.836_U  Ostreococcus_lucimarinus  
#> 3 AY425309.1.1728_U Ostreococcus_lucimarinus  
#> 4 GQ426346.1.1652_U Ostreococcus_tauri        
#> 5 KC583118.1.1764_U Ostreococcus_clade_B      
#> 6 JN862906.1.1568_U Ostreococcus_mediterraneus