Man pages for kevinlkx/Mapgen
Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping
| 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... |
| 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_locus_level_gene_pip | Get locus level gene PIP |
| get_UKBB_region_info | Get region info with filenames of LD matrices and variant... |
| harmonize_sumstats_LD | Harmonize GWAS summary statistics with LD reference |
| LD_diagnosis_susie_rss | Perform diagnosis to check the consistency between the GWAS... |
| load_UKBB_LDREF | Load UK Biobank LD reference matrix and variant information |
| make_genomic_annots | Make genomic annotations from a GTF file |
| match_gwas_bigsnp | Match alleles between GWAS summary statistics and bigSNP... |
| match_gwas_LDREF | Match GWAS sumstats with LD reference files. Only keep... |
| merge_susie_sumstats | merges SuSiE results with original summary statistics data... |
| 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 |
| pipe | Pipe operator |
| 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... |
| 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... |
| 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... |
| snp_view_summary | SNP view summary table |
| susie_finemap_region | Run fine-mapping for one region with SuSiE using summary... |
| track_plot | Make gene track plot using Gviz |
