R: Interface to the 'OpenGWAS' Database API

# Interface to the 'OpenGWAS' Database API

## Documentation for package ‘ieugwasr’ version 1.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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 | OpenGWAS server status
associations | Query specific variants from specific GWAS
batches | Get list of data batches in IEU OpenGWAS database
batch_from_id | Extract batch name from study ID
check_access_token | Check if authentication has been made
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
gwasinfo_files | Get list of download URLs for each file associated with a dataset 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