This version of SolveBio for R is compatible with Vault-based datasets only (released on July 28th, 2017).
This package contains the SolveBio R language bindings. SolveBio makes it easy to access genomic reference data.
Features of this package include:
Please see the SolveBio documentation for more information about the platform.
Installing this package requires an installed R environment.
install.packages("solvebio")
library(solvebio)
# By default it will look for a key in the $SOLVEBIO_API_KEY environment variable.
library(solvebio)
# You may also supply an API key in your code
login(api_key="<Your API key>")
# RStudio users can put the following line in ~/.Rprofile
# Sys.setenv(SOLVEBIO_API_KEY="<Your API key>")
# Retrieve a list of all datasets
datasets <- Dataset.all()
# Retrieve a specific dataset (metadata)
ClinVar <- Dataset.get_by_full_path("solvebio:public:/ClinVar/3.7.4-2017-01-30/Variants-GRCh37")
# Query a dataset with filters as JSON:
filters <- '[["gene_symbol", "BRCA1"]]'
# or, filters as R code:
filters <- list(list('gene_symbol', 'BRCA1'), list('clinical_significance',
'Benign'))
# Execute the queries
# NOTE: paginate=TRUE may issue multiple requests, depending on the dataset and filters
results <- Dataset.query(id = ClinVar$id, filters = filters, limit = 1000, paginate = TRUE)
# Access the results (flattened by default)
results
To use SolveBio in your Shiny app, refer to the docs on Developing Applications with R Shiny and SolveBio.
This package provides a Shiny server wrapper called solvebio::protectedServer() which requires users to authenticate with SolveBio and authorize the app before proceeding. In addition, you may enable token cookie storage by installing ShinyJS and adding JS code (solvebio::protectedServerJS()) to your Shiny UI.
An example app is available in the solvebio-shiny-example GitHub repository.
To install the development version of this package from GitHub, you will need the devtools package.
install.packages(c("devtools", "httr", "jsonlite"))
library(devtools)
devtools::install_github("solvebio/solvebio-r", ref="master")
library(solvebio)
To run the test suite:
Bump the version using the bumpversion command (pip install bumpversion).
Update the NEWS.md with changes.
Update the DESCRIPTION file with the latest date.
Regenerate roxygen2 and build/check the tarball:
make clean make make check
Submit to CRAN.
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