Package: ieugwasr 1.1.0.9000

Gibran Hemani

ieugwasr: Interface to the 'OpenGWAS' Database API

Interface to the 'OpenGWAS' database API <https://api.opengwas.io/api/>. Includes a wrapper to make generic calls to the API, plus convenience functions for specific queries.

Authors:Gibran Hemani [aut, cre, cph], Ben Elsworth [aut], Tom Palmer [aut], Rita Rasteiro [aut]

ieugwasr_1.1.0.9000.tar.gz
ieugwasr_1.1.0.9000.zip(r-4.7)ieugwasr_1.1.0.9000.zip(r-4.6)ieugwasr_1.1.0.9000.zip(r-4.5)
ieugwasr_1.1.0.9000.tgz(r-4.6-any)ieugwasr_1.1.0.9000.tgz(r-4.5-any)
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ieugwasr_1.1.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ieugwasr/json (API)

# Install 'ieugwasr' in R:
install.packages('ieugwasr', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrcieu/ieugwasr/issues

Pkgdown/docs site:https://mrcieu.github.io

On CRAN:

Conda:

11.34 score 109 stars 7 packages 740 scripts 3.6k downloads 31 exports 22 dependencies

Last updated from:645c83f884. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK133
source / vignettesOK180
linux-release-x86_64OK120
macos-release-arm64OK78
macos-oldrel-arm64OK70
windows-develOK67
windows-releaseOK68
windows-oldrelOK77
wasm-releaseOK98

Exports:afl2_chrposafl2_listafl2_rsidapi_queryapi_statusassociationsbatch_from_idbatchescheck_access_tokeneditcheckfill_nget_opengwas_jwtget_query_contentgwasinfogwasinfo_filesinfer_ancestryld_clumpld_clump_localld_matrixld_matrix_localld_reflookuplegacy_idslogging_infophewasselect_apitophitsuservariants_chrposvariants_genevariants_rsidvariants_to_rsid

Dependencies:askpassclicurldplyrgenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR6rlangsystibbletidyselectutf8vctrswithr

Perform fast queries against a massive database of complete GWAS summary data
Authentication | Deprecated Google authentication | Allowance | General API queries | Get API status | Get list of all available studies | Get list of a specific study | Extract particular associations from particular studies | Get the tophits from a study | Perform PheWAS | LD clumping | LD matrix | Variant information | Extracting GWAS summary data based on gene region | 1000 genomes annotations
Rendered fromguide.Rmdusingknitr::rmarkdown

Last update: 2026-05-15
Started: 2019-11-06

Running local LD operations
LD clumping | LD matrix | LD proxies
Rendered fromlocal_ld.Rmdusingknitr::rmarkdown

Last update: 2025-04-07
Started: 2020-06-02

Readme and manuals

Help Manual

Help pageTopics
Look up allele frequencies and LD scores for 1000 genomes populations by chrposafl2_chrpos
Retrieve a allele frequency and LD scores for pre-defined lists of variantsafl2_list
Look up allele frequencies and LD scores for 1000 genomes populations by rsidafl2_rsid
Wrapper for sending queries and payloads to APIapi_query
OpenGWAS server statusapi_status
Query specific variants from specific GWASassociations
Extract batch name from study IDbatch_from_id
Get list of data batches in IEU OpenGWAS databasebatches
Check if authentication has been madecheck_access_token
Check if OpenGWAS allowance needs to be resetcheck_reset
Check datasets that are in process of being uploadededitcheck
Look up sample sizes when meta data is missing from associationsfill_n
Retrieve OpenGWAS JSON Web Token from .Renviron fileget_opengwas_jwt
Parse out json response from httr objectget_query_content
Get list of studies with available GWAS summary statistics through APIgwasinfo
Get list of download URLs for each file associated with a dataset through APIgwasinfo_files
Infer ancestry of GWAS dataset by matching against 1000 genomes allele frequenciesinfer_ancestry
Perform LD clumping on SNP datald_clump
Perform clumping on the chosen variants using the APIld_clump_api
Wrapper for clump function using local plink binary and ld reference datasetld_clump_local
Get LD matrix for list of SNPsld_matrix
Get LD matrix using local plink binary and reference datasetld_matrix_local
Check which rsids are present in a remote LD reference panelld_reflookup
Convert current IDs to legacy IDslegacy_ids
Details of how access token logs are usedlogging_info
Perform fast phewas of a specific variants against all available GWAS datasetsphewas
Print API statusprint.ApiStatus
Print GWAS informationprint.GwasInfo
Toggle API address between development and releaseselect_api
Set the reset time for OpenGWAS allowanceset_reset
Obtain top hits from a GWAS datasettophits
Get user detailsuser
Obtain information about chr pos and surrounding regionvariants_chrpos
Obtain variants around a genevariants_gene
Obtain information about rsidvariants_rsid
Convert mixed array of rsid and chrpos to list of rsidvariants_to_rsid