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rsnps

cran checks R build status Build status codecov.io cran version rstudio mirror downloads

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:

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.

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