In ropensci/rsnps: Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web

rsnps

knitr::opts_chunk$set(
  warning=FALSE,
  message=FALSE,
  comment="#>"
)

This package gives you access to data from OpenSNP and NCBI's dbSNP SNP database.

NOTE

rsnps used to be ropensnp

Data sources

This set of functions/package accesses data from:

• openSNP.org

  • https://opensnp.org
  • See documentation on the openSNP API https://opensnp.org/faq#api
  • See blog post about their API https://opensnp.wordpress.com/2012/01/18/some-progress-on-the-api-json-endpoints/
  • Relevant functions:
    • allgensnp(), allphenotypes(), annotations(), download_users(), fetch_genotypes(), genotypes(), phenotypes(), phenotypes_byid(), users()

• NCBI's dbSNP SNP database

  • See https://www.ncbi.nlm.nih.gov/snp/ for more details
  • Relevant function:
    • ncbi_snp_query()

Install

Install from CRAN

install.packages("rsnps")

Or dev version

install.packages("remotes")
remotes::install_github("ropensci/rsnps")

library("rsnps")

Usage

NCBI dbSNP data

snps <- c("rs332", "rs420358", "rs1837253", "rs1209415715", "rs111068718")
ncbi_snp_query(snps)

The ncbi_snp_query() function can be used with an NCBI API which gives access higher numbers of API requests per second. More information about setting this up can be found in the package help accessed via ?rsnps.

openSNP data

genotypes() function

genotypes('rs9939609', userid='1,6,8', df=TRUE)

phenotypes() function

out <- phenotypes(userid=1)
out$phenotypes$`Hair Type`

For more detail, see the vignette: rsnps tutorial.

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for rsnsps in R doing citation(package = 'rsnps')
• Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

ropensci/rsnps documentation built on July 31, 2023, 11:11 a.m.