Package: rsnps 0.6.1

Julia Gustavsen

rsnps: Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web

A programmatic interface to various 'SNP' 'datasets' on the web: 'OpenSNP' (<https://opensnp.org>), and 'NBCIs' 'dbSNP' database (<https://www.ncbi.nlm.nih.gov/projects/SNP/>). Functions are included for searching for 'NCBI'. For 'OpenSNP', functions are included for getting 'SNPs', and data for 'genotypes', 'phenotypes', annotations, and bulk downloads of data by user.

Authors:Julia Gustavsen [aut, cre], Sina Rüeger [aut], Scott Chamberlain [aut], Kevin Ushey [aut], Hao Zhu [aut]

rsnps_0.6.1.tar.gz
rsnps_0.6.1.zip(r-4.7)rsnps_0.6.1.zip(r-4.6)rsnps_0.6.1.zip(r-4.5)
rsnps_0.6.1.tgz(r-4.6-any)rsnps_0.6.1.tgz(r-4.5-any)
rsnps_0.6.1.tar.gz(r-4.7-any)rsnps_0.6.1.tar.gz(r-4.6-any)
rsnps_0.6.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rsnps/json (API)

# Install 'rsnps' in R:

install.packages('rsnps', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ropensci/rsnps/issues

Pkgdown/docs site:https://docs.ropensci.org

On CRAN:

gene snp sequence api web api-client species dbsnp opensnp ncbi genotype data snps web-api

7.16 score 55 stars 1 packages 73 scripts 53 downloads 4 mentions 19 exports 23 dependencies

Last updated from:1a604aef78 (on master). Checks:10 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	139
pkgdown docs	OK	158
source / vignettes	OK	179
linux-release-x86_64	OK	138
macos-release-arm64	OK	114
macos-oldrel-arm64	OK	119
windows-devel	OK	83
windows-release	OK	72
windows-oldrel	OK	79
wasm-release	OK	133

Exports:allgensnp allphenotypes annotations download_users fetch_genotypes genotypes ld_search LDSearch ncbi_snp_query NCBI_snp_query ncbi_snp_query2 NCBI_snp_query2 ncbi_snp_summary phenotypes phenotypes_byid read_users rsnpsCache tryget users

Dependencies:askpass cli crul curl data.table glue httpcode httr jsonlite lifecycle magrittr mime openssl plyr R6 Rcpp rlang stringi stringr sys triebeard urltools vctrs

rsnps tutorial

Rendered fromrsnps.Rmdusingknitr::knitr

Last update: 2023-07-15
Started: 2020-08-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get SNP (Single-Nucleotide Polymorphism) Data on the Web	rsnps-package rsnps
Get openSNP genotype data for all users at a particular snp.	allgensnp
Get all openSNP phenotypes, their variations, and how many users have data available for a given phenotype.	allphenotypes
Get all openSNP phenotypes, their variations, and how many users have data available for a given phenotype.	annotations
Download openSNP user files.	download_users
Download openSNP genotype data for a user	fetch_genotypes
Get openSNP genotype data for one or multiple users.	genotypes
Internal function to get the frequency of the variants from different studies.	get_frequency
Internal function to get gene names.	get_gene_names
Internal function to get the position, alleles, assembly, hgvs notation	get_placements
Query NCBI's refSNP for information on a set of SNPs via the API	ncbi_snp_query
Get openSNP phenotype data for one or multiple users.	phenotypes
Get all openSNP known variations and all users sharing that phenotype for one phenotype(-ID).	phenotypes_byid
Read in openSNP user files from local storage.	read_users
For use with usethis::use_release_issue()	release_bullets
Defunct functions in rsnps	rsnps-defunct
Get openSNP users.	users