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

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

Author
Scott Chamberlain [aut, cre], Kevin Ushey [aut], Hao Zhu [aut]
Date of publication
2016-11-20 09:22:43
Maintainer
Scott Chamberlain <myrmecocystus@gmail.com>
License
MIT + file LICENSE
Version
0.2.0
URLs

View on CRAN

Man pages

allgensnp
Get genotype data for all users at a particular snp.
allphenotypes
Get all phenotypes, their variations, and how many users have...
annotations
Get all phenotypes, their variations, and how many users have...
download_users
Download openSNP user files.
fetch_genotypes
Download genotype data for a user
flip
Flip Genotypes
genotypes
Get genotype data for one or multiple users.
LDSearch
Search for SNPs in Linkage Disequilibrium with a set of SNPs
NCBI_snp_query
Query NCBI's dbSNP for information on a set of SNPs
NCBI_snp_query2
Query NCBI's dbSNP for information on a set of SNPs
phenotypes
Get phenotype data for one or multiple users.
phenotypes_byid
Get all known variations and all users sharing that phenotype...
read_users
Read in openSNP user files from local storage.
rsnpsCache
rsnps environment
rsnps-package
Get SNP (Single-Nucleotide Polymorphism) Data on the Web
split_to_df
Split a Vector of Strings Following a Regular Structure
swap
Swap Elements in a Vector
tryget
Tryget
users
Get openSNP users.

Files in this package

rsnps
rsnps/inst
rsnps/inst/ignore
rsnps/inst/ignore/ncbi_snp_summary.R
rsnps/inst/doc
rsnps/inst/doc/rsnps_vignette.html
rsnps/inst/doc/rsnps_vignette.Rmd
rsnps/inst/vign
rsnps/inst/vign/rsnps_vignette.md
rsnps/inst/vign/rsnps_vignette.Rmd
rsnps/tests
rsnps/tests/testthat
rsnps/tests/testthat/test-annotations.R
rsnps/tests/testthat/test-NCBI_snp_query.R
rsnps/tests/testthat/test-allphenotypes.R
rsnps/tests/testthat/test-phenotypes.R
rsnps/tests/testthat/test-NCBI_snp_query2.R
rsnps/tests/testthat/test-LDSearch.R
rsnps/tests/testthat/test-phenotypes_byid.R
rsnps/tests/testthat/test-genotypes.R
rsnps/tests/test-all.R
rsnps/NAMESPACE
rsnps/NEWS.md
rsnps/R
rsnps/R/utils.R
rsnps/R/phenotypes.R
rsnps/R/users.R
rsnps/R/NCBI_snp_query2.R
rsnps/R/allphenotypes.R
rsnps/R/genotypes.R
rsnps/R/annotations.R
rsnps/R/fetch_genotypes.R
rsnps/R/allgensnp.R
rsnps/R/phenotypes_byid.R
rsnps/R/download_users.R
rsnps/R/NCBI_snp_query.R
rsnps/R/rsnps-package.R
rsnps/R/LDSearch.R
rsnps/vignettes
rsnps/vignettes/rsnps_vignette.Rmd
rsnps/README.md
rsnps/MD5
rsnps/build
rsnps/build/vignette.rds
rsnps/DESCRIPTION
rsnps/man
rsnps/man/fetch_genotypes.Rd
rsnps/man/LDSearch.Rd
rsnps/man/swap.Rd
rsnps/man/split_to_df.Rd
rsnps/man/annotations.Rd
rsnps/man/phenotypes_byid.Rd
rsnps/man/genotypes.Rd
rsnps/man/NCBI_snp_query2.Rd
rsnps/man/NCBI_snp_query.Rd
rsnps/man/allphenotypes.Rd
rsnps/man/allgensnp.Rd
rsnps/man/rsnpsCache.Rd
rsnps/man/rsnps-package.Rd
rsnps/man/phenotypes.Rd
rsnps/man/tryget.Rd
rsnps/man/flip.Rd
rsnps/man/download_users.Rd
rsnps/man/read_users.Rd
rsnps/man/users.Rd
rsnps/LICENSE