Package: ieugwasr 1.0.1

Gibran Hemani

ieugwasr: Interface to the 'OpenGWAS' Database API

Interface to the 'OpenGWAS' database API <https://gwas-api.mrcieu.ac.uk/>. 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]

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ieugwasr.pdf |ieugwasr.html✨
ieugwasr/json (API)
NEWS

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

Peer review:

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

On CRAN:

10.51 score 72 stars 5 packages 348 scripts 3.6k downloads 30 exports 23 dependencies

Last updated 5 months agofrom:9f4a0bb73d (on v1.0.1). Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-winOKNov 02 2024
R-4.5-linuxOKNov 02 2024
R-4.4-winOKNov 02 2024
R-4.4-macOKNov 02 2024
R-4.3-winOKNov 02 2024
R-4.3-macOKNov 02 2024

Exports:afl2_chrposafl2_listafl2_rsidapi_queryapi_statusassociationsbatch_from_idbatchescheck_access_tokeneditcheckfill_nget_opengwas_jwtget_query_contentgwasinfoinfer_ancestryld_clumpld_clump_localld_matrixld_matrix_localld_reflookuplegacy_idslogging_infophewasselect_apitophitsuservariants_chrposvariants_genevariants_rsidvariants_to_rsid

Dependencies:askpassclicurldplyrfansigenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR6rlangsystibbletidyselectutf8vctrswithr

Perform fast queries against a massive database of complete GWAS summary data

Gibran Hemani

Rendered fromguide.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2024-04-21
Started: 2019-11-06

Running local LD operations

Rendered fromlocal_ld.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2024-03-12
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
MR-Base server statusapi_status
Query specific variants from specific GWASassociations
Extract batch name from study IDbatch_from_id
Get list of data batches in IEU GWAS databasebatches
Check if authentication has been madedcheck_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
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 through 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