Man pages for MRCIEU/ieugwasr
Interface to the 'OpenGWAS' Database API

afl2_chrposLook up allele frequencies and LD scores for 1000 genomes...
afl2_listRetrieve a allele frequency and LD scores for pre-defined...
afl2_rsidLook up allele frequencies and LD scores for 1000 genomes...
api_queryWrapper for sending queries and payloads to API
api_statusMR-Base server status
associationsQuery specific variants from specific GWAS
batchesGet list of data batches in IEU GWAS database
batch_from_idExtract batch name from study ID
check_access_tokenCheck if authentication has been made
dot-datarlang .data
editcheckCheck datasets that are in process of being uploaded
fill_nLook up sample sizes when meta data is missing from...
get_access_tokenGet access token for OAuth2 access to MR Base
get_opengwas_jwtRetrieve OpenGWAS JSON Web Token from .Renviron file
get_query_contentParse out json response from httr object
gwasinfoGet list of studies with available GWAS summary statistics...
infer_ancestryInfer ancestry of GWAS dataset by matching against 1000...
ld_clumpPerform LD clumping on SNP data
ld_clump_apiPerform clumping on the chosen variants using through API
ld_clump_localWrapper for clump function using local plink binary and ld...
ld_matrixGet LD matrix for list of SNPs
ld_matrix_localGet LD matrix using local plink binary and reference dataset
ld_reflookupCheck which rsids are present in a remote LD reference panel
legacy_idsConvert current IDs to legacy IDs
logging_infoDetails of how access token logs are used
phewasPerform fast phewas of a specific variants against all...
pipePipe operator
print.ApiStatusPrint API status
print.GwasInfoPrint GWAS information
revoke_access_tokenRevoke access token for MR Base
select_apiToggle API address between development and release
tophitsObtain top hits from a GWAS dataset
userGet user details
variants_chrposObtain information about chr pos and surrounding region
variants_geneObtain variants around a gene
variants_rsidObtain information about rsid
variants_to_rsidConvert mixed array of rsid and chrpos to list of rsid
MRCIEU/ieugwasr documentation built on April 20, 2024, 11:31 p.m.