Package index • mapgen

All functions
`LD_diagnosis_susie_rss()`	Perform diagnosis to check the consistency between the GWAS z-scores and LD matrix, and detect problematic z-scores (e.g. allele switch issue) using diagnostic functions from SuSiE RSS.
`assign_snp_locus()`	Assign GWAS SNPs to LD blocks
`block_view_summary()`	LD block view summary table
`clean_sumstats()`	Cleans summary statistics
`compute_gene_pip()`	Compute gene PIPs based on fine-mapping result and functional annotations.
`extract_gene_level_result()`	Extract gene-level result from SNP-level gene mapping result
`find_nearest_genes()`	Find the nearest genes for top SNPs in each locus.
`gene_cs()`	Obtain credible gene sets from SNP-level gene mapping table
`gene_manhattan_plot()`	Make gene Manhattan plot
`gene_view_summary()`	Gene view summary table
`get_UKBB_region_info()`	Get region info with filenames of LD matrices and variant information
`get_locus_level_gene_pip()`	Get locus level gene PIP
`harmonize_sumstats_LD()`	Harmonize GWAS summary statistics with LD reference
`load_UKBB_LDREF()`	Load UK Biobank LD reference matrix and variant information
`make_genomic_annots()`	Make genomic annotations from a GTF file
`match_gwas_LDREF()`	Match GWAS sumstats with LD reference files. Only keep variants included in LD reference.
`match_gwas_bigsnp()`	Match alleles between GWAS summary statistics and bigSNP reference panel.
`merge_susie_sumstats()`	merges SuSiE results with original summary statistics data frame
`nearby_interactions()`	Get nearby interactions for enhancer regions near promoters
`partition_pip_annots()`	Partition PIPs into functional annotation categories.
`partition_pip_regions()`	Partition PIPs into disjoint functional annotation regions
`pip_structure_plot()`	Make a structure plot of partitioned PIP by locus
`prepare_susie_data_with_torus_result()`	Prepare summary statistics with TORUS SNP-level priors as input data for SuSiE
`prepare_torus_input_files()`	Prepare TORUS input files
`process_ABC()`	Process ABC scores and save as a GRanges object
`process_finemapping_sumstats()`	Process fine-mapping summary statistics data
`process_gwas_sumstats()`	Process GWAS summary statistics and harmonize with LD reference
`process_loop_data()`	Process chromatin loop data and save as a GRanges object
`process_pcHiC()`	Process PC-HiC data and save as a GRanges object
`read_LD()`	read LD matrix data by file format
`read_LD_SNP_info()`	Read all SNP info in LD reference
`run_finemapping()`	Run functional fine-mapping using summary statistics
`run_torus()`	Run enrichment analysis and compute SNP-level priors using TORUS
`snp_view_summary()`	SNP view summary table
`susie_finemap_region()`	Run fine-mapping for one region with SuSiE using summary statistics (susie_rss)
`track_plot()`	Make gene track plot using Gviz

Reference

All functions