rsnps: Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web
Version 0.2.0

A programmatic interface to various 'SNP' 'datasets' on the web: 'OpenSNP' (), 'NBCIs' 'dbSNP' database (), and Broad Institute 'SNP' Annotation and Proxy Search (). 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.

AuthorScott Chamberlain [aut, cre], Kevin Ushey [aut], Hao Zhu [aut]
Date of publication2016-11-20 09:22:43
MaintainerScott Chamberlain <myrmecocystus@gmail.com>
LicenseMIT + file LICENSE
Version0.2.0
URL https://github.com/ropensci/rsnps
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rsnps")

Getting started

Package overview
README.md

Popular man pages

allphenotypes: Get all phenotypes, their variations, and how many users have...
annotations: Get all phenotypes, their variations, and how many users have...
flip: Flip Genotypes
genotypes: Get genotype data for one or multiple users.
NCBI_snp_query: Query NCBI's dbSNP for information on a set of SNPs
rsnpsCache: rsnps environment
tryget: Tryget
See all...

All man pages Function index File listing

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.

Functions

LDSearch Man page Source code
NCBI_snp_query Man page Source code
NCBI_snp_query2 Man page Source code
allgensnp Man page Source code
allphenotypes Man page Source code
annotations Man page Source code
cuf8 Source code
download_users Man page Source code
fetch_genotypes Man page Source code
flip Man page Source code
genotypes Man page Source code
get_write Source code
ld_search Man page
ncbi_snp_query Man page
ncbi_snp_query2 Man page
osnp_base Source code
parse_data Source code
phenotypes Man page Source code
phenotypes_byid Man page Source code
print.dbsnp Source code
pull_line Source code
pull_vars Source code
read_users Man page Source code
rn Source code
rsnps Man page
rsnps-package Man page
rsnpsCache Man page
rsnps_comp Source code
split_to_df Man page Source code
strtrim Source code
swap Man page Source code
tryget Man page Source code
users Man page Source code

Files

inst
inst/ignore
inst/ignore/ncbi_snp_summary.R
inst/doc
inst/doc/rsnps_vignette.html
inst/doc/rsnps_vignette.Rmd
inst/vign
inst/vign/rsnps_vignette.md
inst/vign/rsnps_vignette.Rmd
tests
tests/testthat
tests/testthat/test-annotations.R
tests/testthat/test-NCBI_snp_query.R
tests/testthat/test-allphenotypes.R
tests/testthat/test-phenotypes.R
tests/testthat/test-NCBI_snp_query2.R
tests/testthat/test-LDSearch.R
tests/testthat/test-phenotypes_byid.R
tests/testthat/test-genotypes.R
tests/test-all.R
NAMESPACE
NEWS.md
R
R/utils.R
R/phenotypes.R
R/users.R
R/NCBI_snp_query2.R
R/allphenotypes.R
R/genotypes.R
R/annotations.R
R/fetch_genotypes.R
R/allgensnp.R
R/phenotypes_byid.R
R/download_users.R
R/NCBI_snp_query.R
R/rsnps-package.R
R/LDSearch.R
vignettes
vignettes/rsnps_vignette.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/fetch_genotypes.Rd
man/LDSearch.Rd
man/swap.Rd
man/split_to_df.Rd
man/annotations.Rd
man/phenotypes_byid.Rd
man/genotypes.Rd
man/NCBI_snp_query2.Rd
man/NCBI_snp_query.Rd
man/allphenotypes.Rd
man/allgensnp.Rd
man/rsnpsCache.Rd
man/rsnps-package.Rd
man/phenotypes.Rd
man/tryget.Rd
man/flip.Rd
man/download_users.Rd
man/read_users.Rd
man/users.Rd
LICENSE
rsnps documentation built on May 19, 2017, 7:33 a.m.

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