Function reference
-
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
-
batch_from_id() - Extract batch name from study ID
-
batches() - Get list of data batches in IEU GWAS database
-
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