Interface to the 'OpenGWAS' Database API

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Documentation for package ‘ieugwasr’ version 1.0.0

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afl2_chrpos Look up allele frequencies and LD scores for 1000 genomes populations by chrpos
afl2_list Retrieve a allele frequency and LD scores for pre-defined lists of variants
afl2_rsid Look up allele frequencies and LD scores for 1000 genomes populations by rsid
api_query Wrapper for sending queries and payloads to API
api_status MR-Base server status
associations Query specific variants from specific GWAS
batches Get list of data batches in IEU GWAS database
batch_from_id Extract batch name from study ID
check_access_token Check if authentication has been maded
editcheck Check datasets that are in process of being uploaded
fill_n Look up sample sizes when meta data is missing from associations
get_opengwas_jwt Retrieve OpenGWAS JSON Web Token from .Renviron file
get_query_content Parse out json response from httr object
gwasinfo Get list of studies with available GWAS summary statistics through API
infer_ancestry Infer ancestry of GWAS dataset by matching against 1000 genomes allele frequencies
ld_clump Perform LD clumping on SNP data
ld_clump_api Perform clumping on the chosen variants using through API
ld_clump_local Wrapper for clump function using local plink binary and ld reference dataset
ld_matrix Get LD matrix for list of SNPs
ld_matrix_local Get LD matrix using local plink binary and reference dataset
ld_reflookup Check which rsids are present in a remote LD reference panel
legacy_ids Convert current IDs to legacy IDs
logging_info Details of how access token logs are used
phewas Perform fast phewas of a specific variants against all available GWAS datasets
print.ApiStatus Print API status
print.GwasInfo Print GWAS information
select_api Toggle API address between development and release
tophits Obtain top hits from a GWAS dataset
user Get user details
variants_chrpos Obtain information about chr pos and surrounding region
variants_gene Obtain variants around a gene
variants_rsid Obtain information about rsid
variants_to_rsid Convert mixed array of rsid and chrpos to list of rsid