This package gives you access to data from OpenSNP and NCBI’s dbSNP SNP database.
rsnps
used to be ropensnp
This set of functions/package accesses data from:
allgensnp()
, allphenotypes()
, annotations()
,
download_users()
, fetch_genotypes()
, genotypes()
,
phenotypes()
, phenotypes_byid()
, users()
ncbi_snp_query()
Install from CRAN
install.packages("rsnps")
Or dev version
install.packages("remotes")
remotes::install_github("ropensci/rsnps")
library("rsnps")
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 rs1219… "CFT… TTT, d… TTT
#> 2 rs420358 1 40341239 snv rs4203… "" A,C,G,T A
#> 3 rs1837253 5 111066174 snv rs1837… "" T,C T
#> 4 rs1209415715 9 41782316 snv rs1209… "" T,A,C T
#> # ℹ 8 more variables: variation_allele <chr>, seqname <chr>, hgvs <chr>,
#> # assembly <chr>, ref_seq <chr>, minor <chr>, maf <dbl>,
#> # maf_population <list>
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
.
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.
rsnsps
in R doing
citation(package = 'rsnps')