rsnps (version 0.6.0)

rsnps-package: Get SNP (Single-Nucleotide Polymorphism) Data on the Web

Description

This package gives you access to data from OpenSNP (https://opensnp.org) via their API (https://opensnp.org/faq#api) and NCBI's dbSNP SNP database (https://www.ncbi.nlm.nih.gov/snp).

NCBI Authentication

This applies the function ncbi_snp_query():

You can optionally use an API key, if you do it will allow higher rate limits (more requests per time period)

To get an API key from NCBI you can login to create a key via your account settings at https://www.ncbi.nlm.nih.gov/account/settings/

#' Note: NCBI login is via with a 3rd party account (e.g. Google, orcid, etc.). If you had an already existing NCBI account you can link it with a 3rd party login and then you can retire your old NCBI login if you haven't already), otherwise just #' create a new account.

Once you are logged on to your NCBI account settings (https://www.ncbi.nlm.nih.gov/account/settings/) you can go to the section "API Key Management"

Here you can select "Create an API Key" (which will give you up to 10 requests per second, instead of the 3 per second without the API key.).

After generating your key, set an environment variable as ENTREZ_KEY in .Renviron. This .Renviron file can be edited using usethis::edit_r_environ() or by locating and creating/editing this file yourself.

ENTREZ_KEY='youractualkeynotthisstring'

Once the API is added to your .Renviron file you can then restart R for this to take effect.

You can optionally pass in your API key to the key parameter in NCBI functions in this package. However, it's much better from a security perspective to set an environment variable.

Author

Scott Chamberlain

Kevin Ushey

Hao Zhu

Sina Rüeger

Julia Gustavsen