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

By default, will be version GRCh38:

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>

For version GRCh37:

snps <- c("rs332", "rs420358", "rs1837253", "rs1209415715", "rs111068718")
ncbi_snp_query(snps, "37")

#> A tibble: 4 x 16
#> query     chromosome     bp class rsid  gene  alleles ancestral_allele variation_allele seqname hgvs assembly ref_seq
#> <chr>     <chr>       <dbl> <chr> <chr> <chr> <chr>   <chr>            <chr>            <chr>   <chr> <chr>    <chr>  
#> 1 rs332     7          1.17e8 del   rs12~ "CFT~ TTT, d~ TTT              delTTT           NC_000~ NC_0~ GRCh37.~ NA     
#> 2 rs420358  1          4.08e7 snv   rs42~ ""    A,C,G,T A                C,G,T            NC_000~ NC_0~ GRCh37.~ NA     
#> 3 rs1837253 5          1.10e8 snv   rs18~ ""    T,C     T                C                NC_000~ NC_0~ GRCh37.~ T      
#>4 rs120941~ 9          4.72e7 snv   rs12~ ""    T,A,C   T                A,C              NC_000~ NC_0~ GRCh37.~ NA     
#> # ... with 3 more variables: 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.