README.md

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

rsnps

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)

#> # A tibble: 4 × 16
#>   query        chromosome        bp class rsid   gene   alleles ancestral_allele
#>   <chr>        <chr>          <dbl> <chr> <chr>  <chr>  <chr>   <chr>           
#> 1 rs332        7          117559593 del   rs121… "CFTR… TTT, d… TTT             
#> 2 rs420358     1           40341239 snv   rs420… ""     A,C,G,T A               
#> 3 rs1837253    5          111066174 snv   rs183… ""     T,C     T               
#> 4 rs1209415715 9           41782316 snv   rs120… ""     T,A,C   T               
#> # … with 8 more variables: variation_allele <chr>, seqname <chr>, hgvs <chr>,
#> #   assembly <chr>, ref_seq <chr>, minor <chr>, maf <dbl>,
#> #   maf_population <list>

openSNP data

genotypes() function

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

#>    snp_name snp_chromosome snp_position                 user_name user_id
#> 1 rs9939609             16     53786615 Bastian Greshake Tzovaras       1
#> 2 rs9939609             16     53786615              Nash Parovoz       6
#> 3 rs9939609             16     53786615         Samantha B. Clark       8
#>   genotype_id genotype
#> 1           9       AT
#> 2           5       AT
#> 3           2       TT

phenotypes() function

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

#> $phenotype_id
#> [1] 16
#> 
#> $variation
#> [1] "straight"

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.

rsnps documentation built on Jan. 28, 2022, 5:07 p.m.