SolveBio for R

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:

• Authentication with SolveBio's API
• REST API query support
• S3 object system for SolveBio API resources
• Portability between most platforms: Linux, Windows, OS X.

Please see the SolveBio documentation for more information about the platform.

Installation

Installing this package requires an installed R environment.

install.packages("solvebio")
library(solvebio)

Usage

# 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

Shiny

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.

Developers

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:

make test

Packaging and Releasing

1. Bump the version using the bumpversion command (pip install bumpversion).

2. Update the NEWS.md with changes.

3. Update the DESCRIPTION file with the latest date.

4. Regenerate roxygen2 and build/check the tarball:

   make clean make make check

5. Submit to CRAN.