Package index
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manhattan_plot() - Manhattan plot
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qq_plot() - QQ plot for GWAS p-values
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miami_plot() - Miami plot (mirrored Manhattan)
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locus_plot() - Locus zoom plot
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volcano_plot() - GWAS effect-size volcano plot
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pvalue_heatmap() - Genome-wide p-value heatmap
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circular_manhattan() - Circular Manhattan plot
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gwas_summary() - GWAS Summary Panel
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enrichment_manhattan() - Enrichment Manhattan plot
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multitrait_manhattan() - Multi-trait Manhattan plot
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phewas_plot() - PheWAS plot
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coloc_plot() - Colocalization locus plot
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finemapping_plot() - Fine-mapping credible set plot
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genetic_correlation() - Genetic correlation matrix
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architecture_plot() - Genetic architecture plot
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snp_density() - SNP density karyogram
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density_signal_plot() - Density–signal dual-track plot
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chr_info_human()chr_info_mouse()chr_info_cattle() - Chromosome information for common species
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chr_info_ucsc() - Fetch chromosome information from UCSC
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manhattan_genes() - Add gene labels to a Manhattan plot
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annotate_genes() - Annotate peaks with nearest gene names
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highlight_regions() - Add highlighted regions to a Manhattan plot
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top_hits() - Extract top hits from GWAS results
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read_gwas_table() - Read GWAS summary statistics from any tabular file
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read_plink_assoc() - Read PLINK association results
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read_plink_linear() - Read PLINK linear regression results
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read_plink_logistic() - Read PLINK logistic regression results
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read_regenie() - Read REGENIE results
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read_gcta_mlma() - Read GCTA MLMA results
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read_gemma() - Read GEMMA association results
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as_gwas_data() - Create a gwas_data object
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validate_gwas_data() - Validate a gwas_data object
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theme_gwas() - Minimal GWAS theme for ggplot2
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theme_nature()theme_science()theme_plos()theme_cell()theme_presentation()theme_poster() - Journal-specific themes for GWAS plots
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gwas_palette() - GWAS Color Palettes
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gwas_palettes() - List available GWAS palettes
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gwas_preset() - GWAS plot presets
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scale_color_chromosome()scale_fill_chromosome() - Chromosome color scale
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scale_color_gwas()scale_fill_gwas() - Colorblind-safe chromosome color scale
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filter_region() - Filter variants by genomic region
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maf_filter() - Filter variants by minor allele frequency
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merge_gwas() - Merge multiple GWAS datasets
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get_loci() - Get significant loci
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calc_lambda() - Calculate genomic inflation factor (lambda GC)
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example_gwas - Example GWAS dataset