rOpenSci: The rsnps package

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)

#>          query chromosome        bp class         rsid          gene
#> 1        rs332          7 117559593   del  rs121909001 CFTR/CFTR-AS1
#> 2     rs420358          1  40341239   snv     rs420358              
#> 3    rs1837253          5 111066174   snv    rs1837253              
#> 4 rs1209415715          9  41782316   snv rs1209415715              
#>       alleles ancestral_allele variation_allele      seqname
#> 1 TTT, delTTT              TTT           delTTT NC_000007.14
#> 2     A,C,G,T                A            C,G,T NC_000001.11
#> 3         T,C                T                C NC_000005.10
#> 4         T,C                T                C NC_000009.12
#>                                                                               hgvs
#> 1                                            NC_000007.14:g.117559593_117559595del
#> 2 NC_000001.11:g.40341239A>C,NC_000001.11:g.40341239A>G,NC_000001.11:g.40341239A>T
#> 3                                                      NC_000005.10:g.111066174T>C
#> 4                                                       NC_000009.12:g.41782316T>C
#>     assembly ref_seq minor    maf
#> 1 GRCh38.p12    <NA>  <NA>     NA
#> 2 GRCh38.p12       A     C 0.8614
#> 3 GRCh38.p12       T     C 0.7133
#> 4 GRCh38.p12    <NA>  <NA>     NA

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.