Package index • gwasplot

All functions

annotate_with_centromere(): Annotate data with centromere information

annotate_with_chip_genes(<GWASFormatter>): Annotate top hits with CHIP gene information

annotate_with_chip_genes(): Annotate data with CHIP gene information

annotate_with_immunoglobulin(): Annotate data with immunoglobulin gene information

append_ashr_results(): Append lfsr results from ashr to a data frame

assign_gene_tracks(): Assign genes to tracks to avoid overlaps

compute_sample(): Take a random sample of rows from the summary stats table

db_connect(): Connect to DuckDB

exclude_difficult_regions(): Exclude difficult regions

filter_variants(): Filter variants

find_nearest_gene(): Find the nearest gene for variants

get_biosample_for_accession(): Get biosample to accession mapping for a specific accession

get_encode_biosamples(): Get available ENCODE SCREEN biosamples for a given assembly

locuszoom(): LocusZoom-style plot for GWAS results

manhattan(): Plot a Manhattan plot from a gwas object

qqplot(): QQ plot for p-values

qqplot_save(): Save a QQ plot of GWAS p-values

query_encode_ccres(): Query ENCODE SCREEN cCREs for a genomic region

query_ot_api_variants(): Query Open Targets Genetics API for variant information

reformat_names(): Rename columns in the dataset to standard names

reformat_summary_statistics(): Reformat GWAS summary statistics from regenie or SAIGE

search_cell_types(): Search for available cell types and their biosample IDs

select_top_hits(): Pull top hits from a GWASFormatter or a data.frame/tibble

volcano(): Volcano plot for GWAS results