Interface to the 'OpenGWAS' Database API

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Documentation for package ‘ieugwasr’ version 1.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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
check_reset	Check if OpenGWAS allowance needs to be reset
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
set_reset	Set the reset time for OpenGWAS allowance
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