R language bindings for SolveBio's API. SolveBio is a biomedical knowledge hub that enables life science organizations to collect and harmonize the complex, disparate "multi-omic" data essential for today's R&D and BI needs. For more information, visit < https://www.solvebio.com>.
PLEASE NOTE: The SolveBio R Bindings are currently in alpha. The bindings may change frequently so please check back for updates.
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.
To install the development version of this package from GitHub, you will need the
install.packages(c("devtools", "httr", "jsonlite"))library(devtools)devtools::install_github("solvebio/solvebio-r")library(solvebio)
# By default it will look for a key in the $SOLVEBIO_API_KEY environment variable.require(solvebio)# You may also supply an API key in your codelogin(api_key="<Your SolveBio API key>")# Retrieve a list of all datasetsdatasets = Dataset.all()# Retrieve a specific dataset (metadata)dataset = Dataset.retrieve('ClinVar/Variants')# 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 filtersresults = Dataset.query('ClinVar/3.7.2-2016-08-02/Variants', filters=filters, limit=1000, paginate=TRUE)# Access the results (flattened by default)results