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