Man pages for RajLabMSSM/echofinemap
echoverse module: Fine-mapping functions
| ABF | Fine-map with ABF |
| check_args | Check arguments |
| check_required_cols | Check for necessary columns |
| COJO | Run _GCTA-COJO_ |
| COJO_args | COJO arguments |
| COJO_find_executable | COJO: find executable |
| COJO_get_stepwise_results | Gather stepwise conditional results |
| COJO_locus_subdir | Make _GCTA-COJO_ path |
| COJO_process_results | Gather all _GCTA-COJO_ results |
| COJO_run | Run _GCTA-COJO_ |
| create_method_path | Create method path |
| drop_finemap_cols | Drop fine-mapping columns |
| FINEMAP | Fine-map locus with 'FINEMAP' |
| FINEMAP_construct_data | Prepare input files for 'FINEMAP' |
| FINEMAP_construct_master | Construct the 'FINAMAP' master file |
| FINEMAP_find_executable | Find FINEMAP executable |
| FINEMAP_import_log | Import log |
| FINEMAP_process_results | FINEMAP: process results |
| get_data | Get data |
| get_pheno_variance | Compute phenotype variance |
| install_submodule_git | Install a submodule |
| is_32bit | Checks whether OS is a 32-bit Windows |
| lfm | List fine-mapping methods |
| multifinemap | Multi-fine-map |
| multifinemap_handler | Fine-map using multiple fine-mapping tools |
| multifinemap_handler_method | Multi-finemap handler: select fine-mapping method |
| PAINTOR | PAINTOR: fine-map |
| PAINTOR_create_locus_file | Create QTL locus file for PAINTOR |
| PAINTOR_datatype_handler | Determine data types (GWAS, QTL) |
| PAINTOR_download_annotations | Download annotations for PAINTOR |
| PAINTOR_install | Install PAINTOR via command line |
| PAINTOR_prepare_annotations | Prepare PAINTOR annotations |
| PAINTOR_prepare_ld_multiancestry | Prepare multi-ancestry LD files for PAINTOR |
| PAINTOR_process_results | PAINTOR: process results |
| PAINTOR_run | Run PAINTOR |
| PAINTOR_sample_data | Find PAINTOR sample data |
| POLYFUN | Run PolyFun+SUSIE fine-mapping pipeline |
| POLYFUN_check_version | POLYFUN: check version |
| POLYFUN_compute_priors | PolyFun: recompute priors |
| POLYFUN_download_ref_files | Download reference files |
| POLYFUN_find_folder | Find PolyFun folder |
| POLYFUN_finemapper | Run _PolyFun+SUSIE_ fine-mapping pipeline |
| POLYFUN_gather_annotations | Find and import PolyFun annotation files |
| POLYFUN_gather_ldscores | Find and import LD score files |
| POLYFUN_help | POLYFUN help |
| POLYFUN_import_priors | Import pre-computed priors |
| POLYFUN_initialize | PolyFun: Initialize |
| POLYFUN_install | Install PolyFun |
| POLYFUN_munge_summ_stats | PolyFun: Munge summary stats |
| POLYFUN_prepare_snp_input | Prepare SNP input for PolyFun |
| POLYFUN_read_priors | Read priors |
| POLYFUN_run_ldsc | Run a modified version of S-LDSC |
| prepare_priors | Prepare priors |
| rbind_filelist | Bind stored files |
| remove_dup_snps | Remove duplicate SNPs |
| remove_na_rows | Remove NA rows |
| required_cols | Table of required columns |
| setup_gcc | Setup gcc |
| SUSIE | Fine-map with SUSIE |
| SUSIE_get_func | Get susieR fine-mapping function |
| SUSIE_run | Run 'susieR' fine-mapping |
