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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:

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   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.

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.

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  • 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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Version

Install

install.packages('rsnps')

Monthly Downloads

125

Version

0.6.0

License

MIT + file LICENSE

Issues

Pull Requests

Stars

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Maintainer

Last Published

June 30th, 2023

Functions in rsnps (0.6.0)

get_placements

Internal function to get the position, alleles, assembly, hgvs notation
read_users

Read in openSNP user files from local storage.
phenotypes_byid

Get all openSNP known variations and all users sharing that phenotype for one phenotype(-ID).
users

Get openSNP users.
tryget

Tryget
ld_search

This function is defunct.
swap

Swap Elements in a Vector
split_to_df

Split a Vector of Strings Following a Regular Structure
flip

Flip Genotypes
genotypes

Get openSNP genotype data for one or multiple users.
allgensnp

Get openSNP genotype data for all users at a particular snp.
allphenotypes

Get all openSNP phenotypes, their variations, and how many users have data available for a given phenotype.
download_users

Download openSNP user files.
fetch_genotypes

Download openSNP genotype data for a user
annotations

Get all openSNP phenotypes, their variations, and how many users have data available for a given phenotype.
release_bullets

For use with usethis::use_release_issue()
phenotypes

Get openSNP phenotype data for one or multiple users.
ncbi_snp_query

Query NCBI's refSNP for information on a set of SNPs via the API
rsnps-defunct

Defunct functions in rsnps
NCBI_snp_query2

This function is defunct.
ncbi_snp_summary

This function is defunct.
LDSearch

This function is defunct.
get_gene_names

Internal function to get gene names.
get_frequency

Internal function to get the frequency of the variants from different studies.
rsnps-package

Get SNP (Single-Nucleotide Polymorphism) Data on the Web
rsnpsCache

rsnps environment