The hapiverse (human API universe) is a metapackage whose goal is embrace a collection of R packages that work together to provide programmatic access to the European Bioinformatics Institute (EMBL-EBI) REST API services, namely those related with human genetic variation and phenotypes. Currently, the hapiverse provides easy installation and loading of two packages:
- gwasrapidd that provides access to the GWAS Catalog
- quincunx that provides access to the PGS Catalog
You can install the current version of hapiverse with:
# install.packages("remotes")
remotes::install_github("maialab/hapiverse")After installing hapiverse, you also get gwasrapidd and quincunx installed.
To load and attach concomitantly gwasrapidd and quincunx simply run:
library(hapiverse)
#> ── Attaching packages ─────────────────────────────────────── hapiverse 0.1.0 ──
#> ✓ gwasrapidd 0.99.11 ✓ quincunx 0.1.0
#> ── Conflicts ────────────────────────────────────────── hapiverse_conflicts() ──
#> x quincunx::bind() masks gwasrapidd::bind()
#> x quincunx::get_traits() masks gwasrapidd::get_traits()
#> x quincunx::intersect() masks gwasrapidd::intersect(), base::intersect()
#> x quincunx::n() masks gwasrapidd::n()
#> x quincunx::open_in_dbsnp() masks gwasrapidd::open_in_dbsnp()
#> x quincunx::open_in_pubmed() masks gwasrapidd::open_in_pubmed()
#> x quincunx::setdiff() masks gwasrapidd::setdiff(), base::setdiff()
#> x quincunx::setequal() masks gwasrapidd::setequal(), base::setequal()
#> x quincunx::union() masks gwasrapidd::union(), base::union()During the attaching of hapiverse, you will get notified of those
functions that have clashing names. Behind the scenes we use the package
conflicted to avoid misuse of
functions with the same name. In these cases you will be required to
choose one of the functions by using the double colon operator (::).
As an example, both gwasrapidd and quincunx provide a function named
get_traits(). If you try to use it directly, R will throw an error and
ask that you specify either gwasrapidd::get_traits() or
quincunx::get_traits().
Trying to use get_traits() will return an error because of the
ambiguity arising from the two definitions:
get_traits()
#> Error: [conflicted] `get_traits` found in 2 packages.
#> Either pick the one you want with `::`
#> * quincunx::get_traits
#> * gwasrapidd::get_traits
#> Or declare a preference with `conflict_prefer()`
#> * conflict_prefer("get_traits", "quincunx")
#> * conflict_prefer("get_traits", "gwasrapidd")Note that you can use the function hapiverse_conflicts() at any time
to revise the list of clashing function names:
hapiverse_conflicts()
#> ── Conflicts ────────────────────────────────────────── hapiverse_conflicts() ──
#> x quincunx::bind() masks gwasrapidd::bind()
#> x quincunx::get_traits() masks gwasrapidd::get_traits()
#> x quincunx::intersect() masks gwasrapidd::intersect(), base::intersect()
#> x quincunx::n() masks gwasrapidd::n()
#> x quincunx::open_in_dbsnp() masks gwasrapidd::open_in_dbsnp()
#> x quincunx::open_in_pubmed() masks gwasrapidd::open_in_pubmed()
#> x quincunx::setdiff() masks gwasrapidd::setdiff(), base::setdiff()
#> x quincunx::setequal() masks gwasrapidd::setequal(), base::setequal()
#> x quincunx::union() masks gwasrapidd::union(), base::union()If you specify the package name with the double colon operator (::),
then the ambiguity is resolved and execution proceeds normally. Using
get_traits() from gwasrapidd:
gwasrapidd::get_traits(efo_id = 'EFO_0005537')
#> An object of class "traits" (from package "gwasrapidd")
#> Slot "traits":
#> # A tibble: 1 x 3
#> efo_id trait uri
#> <chr> <chr> <chr>
#> 1 EFO_0005537 triple-negative breast cancer http://www.ebi.ac.uk/efo/EFO_0005537Or using get_traits() provided by quincunx:
quincunx::get_traits(efo_id = 'EFO_0005537')
#> An object of class "traits" (from package "quincunx")
#> Slot "traits":
#> # A tibble: 1 x 6
#> efo_id parent_efo_id is_child trait description url
#> <chr> <chr> <lgl> <chr> <chr> <chr>
#> 1 EFO_00… <NA> FALSE triple-ne… An invasive breast carc… http://www…
#>
#> Slot "pgs_ids":
#> # A tibble: 1 x 4
#> efo_id parent_efo_id is_child pgs_id
#> <chr> <chr> <lgl> <chr>
#> 1 EFO_0005537 <NA> FALSE PGS000216
#>
#> Slot "child_pgs_ids":
#> # A tibble: 0 x 4
#> # … with 4 variables: efo_id <chr>, parent_efo_id <chr>, is_child <lgl>,
#> # child_pgs_id <chr>
#>
#> Slot "trait_categories":
#> # A tibble: 1 x 4
#> efo_id parent_efo_id is_child trait_categories
#> <chr> <chr> <lgl> <chr>
#> 1 EFO_0005537 <NA> FALSE Cancer
#>
#> Slot "trait_synonyms":
#> # A tibble: 5 x 4
#> efo_id parent_efo_id is_child trait_synonyms
#> <chr> <chr> <lgl> <chr>
#> 1 EFO_0005537 <NA> FALSE TN breast cancer
#> 2 EFO_0005537 <NA> FALSE Triple-Negative Breast Carcinoma
#> 3 EFO_0005537 <NA> FALSE triple-negative breast cancer
#> 4 EFO_0005537 <NA> FALSE triple-negative breast carcinoma
#> 5 EFO_0005537 <NA> FALSE triple-receptor negative breast cancer
#>
#> Slot "trait_mapped_terms":
#> # A tibble: 7 x 4
#> efo_id parent_efo_id is_child trait_mapped_terms
#> <chr> <chr> <lgl> <chr>
#> 1 EFO_0005537 <NA> FALSE DOID:0060081
#> 2 EFO_0005537 <NA> FALSE MESH:D064726
#> 3 EFO_0005537 <NA> FALSE MONDO:0005494
#> 4 EFO_0005537 <NA> FALSE NCIT:C71732
#> 5 EFO_0005537 <NA> FALSE SCTID:706970001
#> 6 EFO_0005537 <NA> FALSE SNOMEDCT:706970001
#> 7 EFO_0005537 <NA> FALSE UMLS:C3539878