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
rsnspsin R doingcitation(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.
