This package gives you access to data from OpenSNP and NCBI’s dbSNP SNP database.
This set of functions/package accesses data from:
Install from CRAN
install.packages("rsnps")
Or dev version
install.packages("remotes")
remotes::install_github("ropensci/rsnps")
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
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`
For more detail, see the vignette: rsnps tutorial.
rsnsps
in R doing citation(package = 'rsnps')