Package index
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annotate_variants_ensembl() - Annotate variants with functional consequences using Ensembl VEP API
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annotate_with_centromere() - Annotate data with centromere information
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annotate_with_chip_genes(<GWASFormatter>) - Annotate top hits with CHIP gene information
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annotate_with_chip_genes() - Annotate data with CHIP gene information
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annotate_with_immunoglobulin() - Annotate data with immunoglobulin gene information
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annotate_with_l2g() - Annotate top GWAS hits with Open Targets Locus-to-Gene (L2G) predictions
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append_ashr_results() - Append lfsr results from ashr to a data frame
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assign_gene_tracks() - Assign genes to tracks to avoid overlaps
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compute_sample() - Take a random sample of rows from the summary stats table
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db_connect() - Connect to DuckDB
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exclude_difficult_regions() - Exclude difficult regions
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filter_variants() - Filter variants
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find_nearest_gene() - Find the nearest gene for variants
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get_biosample_for_accession() - Get biosample to accession mapping for a specific accession
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get_encode_biosamples() - Get available ENCODE SCREEN biosamples for a given assembly
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identify_loci() - Identify independent GWAS loci using a greedy, distance-based algorithm
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lambda_gc() - Compute the genomic inflation factor (lambda GC)
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locuszoom() - LocusZoom-style plot for GWAS results
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manhattan() - Plot a Manhattan plot from a gwas object
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qqplot() - QQ plot for GWAS p-values
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query_encode_ccres() - Query ENCODE SCREEN cCREs for a genomic region
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query_ot_api_v2g() - Query Open Targets Platform API for Locus-to-Gene (L2G) predictions
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query_ot_api_variants() - Query Open Targets Platform API for variant information
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reformat_names() - Rename columns in the dataset to standard names
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reformat_summary_statistics() - Reformat GWAS summary statistics from regenie or SAIGE
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search_cell_types() - Search for available cell types and their biosample IDs
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select_top_hits() - Pull top hits from a GWASFormatter or a data.frame/tibble
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volcano() - Volcano plot for GWAS results