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]

ieugwasr_1.0.1.tar.gz
ieugwasr_1.0.1.tar.gz(r-4.5-noble)ieugwasr_1.0.1.tar.gz(r-4.4-noble)
ieugwasr_1.0.1.tgz(r-4.4-emscripten)ieugwasr_1.0.1.tgz(r-4.3-emscripten)
ieugwasr.pdf |ieugwasr.html✨
ieugwasr/json (API)
NEWS

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

Peer review:

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

30 exports 1.64 score 23 dependencies 5 dependents 5.1k downloads

Last updated 4 days agofrom:e95576bf2d

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 Jul 02 2024.

Last update: 2024-04-23
Started: 2024-03-26

Running local LD operations

Rendered fromlocal_ld.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2024-03-26
Started: 2024-03-26

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