Man pages for jwr-git/mrpipeline
Implements a Ready-for-Use Mendelian Randomisation Pipeline
| annotate_data | Annotates the data using given IDs |
| annotate_efo | Annotate diseases with EFO IDs |
| annotate_ensg | Annotate ENSG IDs with gene names |
| calc_f_stat | Calculate F-statistic |
| check_snps | Check if SNPs are good for use in analyses and mark them as... |
| cis_trans | Annotate cis/trans SNPs |
| combine_results | Combine MR and coloc results into one data.frame |
| dat_to_gwasvcf | Convert data.frame to gwasvcf format. |
| do_coloc | Run colocalisation analyses |
| do_mr | Run Mendelian randomisation analyses |
| dot-calc_pve | Calculate PVE |
| dot-cdat_from_mixed | Helper function to extract colocalisation regions for when... |
| dot-chunk | Splits vector into chunks |
| dot-coloc_sub | Sub-function for the colocalisation analyses |
| dot-coloc_susie_sub | Sub function to run SuSiE and coloc |
| dot-dgidb_linkage | Link ENSG IDs with DGIdb |
| dot-ensg_to_name | Convert ENSG IDs -> gene names |
| dot-gwasvcf_to_coloc_rsid | Prepare gwasvcf files for coloc. This method will extract... |
| dot-gwasvcf_to_pwcoco | Prepare gwasvcf files for PWCoCo |
| dot-ieugwasr_to_pwcoco | Prepare ieugwasr data for PWCoCo |
| dot-ivw_delta | IVW weighted delta |
| dot-print_msg | Helper function for message printing. |
| dot-pwcoco_sub | Sub-function to run PWCoCo |
| dot-read_dataset | Read datasets |
| dot-wr_taylor_approx | WR Taylor Approx of SE |
| drug_target_evidence | Generate drug target evidence |
| extract_matched_regions | Extract SNPs based on region for colocalisation analyses. Can... |
| file_to_gwasvcf | Convert file(s) to gwasvcf format. |
| forest_plot | Forest plot |
| get_col_name | Get column names from agnostic but formatted data.frame |
| harmonise | Harmonise exposure and outcomes. |
| hello | Hello, World! |
| is_ambiguous | Check if SNP frequencies are ambiguous |
| is_palindromic | Check if SNP is palindromic |
| mr_pipeline | Entry point for the pipeline. |
| pairwise_analysis | Performs pairwise harmonisation and analyses - helpful when... |
| read_exposure | Read exposures |
| read_outcome | Read outcomes |
| reexports | Objects exported from other packages |
| regional_plot | Plots a regional plot of the area being tested for... |
| validate_config | Validates parameters in config file |
| volcano_plot | Volcano plot |
| z_comparison_plot | Z score comparison plot |
| z_plot | Z plot |
