Man pages for MRCIEU/TwoSampleMR
Two Sample MR Functions and Interface to MR Base Database
| add_metadata | Add meta data to extracted data |
| add_rsq | Estimate r-square of each association |
| allele_frequency | Estimate allele frequency from SNP |
| available_outcomes | Get list of studies with available GWAS summary statistics... |
| cleanup_outcome_data | Avoid issues in MR by finding impossible vals and setting to... |
| clump_data | Perform LD clumping on SNP data |
| combine_all_mrresults | Combine all mr results |
| combine_data | Combine data |
| contingency | Obtain 2x2 contingency table from marginal parameters and... |
| convert_outcome_to_exposure | Convert outcome data to exposure data |
| create_label | Create fixed width label |
| dat_to_MRInput | Convert TwoSampleMR format to MendelianRandomization format |
| dat_to_RadialMR | Convert dat to RadialMR format |
| default_parameters | List of parameters for use with MR functions |
| directionality_test | Perform MR Steiger test of directionality |
| effective_n | Estimate the effective sample size in a case control study |
| enrichment | Perform enrichment analysis |
| enrichment_method_list | Get list of available p-value enrichment methods |
| estimate_trait_sd | Estimate trait SD by obtaining beta estimates from z-scores... |
| extract_instruments | Find instruments for use in MR from the MR Base database |
| extract_outcome_data | Supply the output from 'read_exposure_data()' and all the... |
| fishers_combined_test | Fisher's combined test |
| forest_plot | Forest plot for multiple exposures and multiple outcomes |
| forest_plot_1_to_many | 1-to-many forest plot |
| forest_plot_basic | A basic forest plot |
| forest_plot_basic2 | A basic forest plot |
| format_1_to_many | Format MR results for a 1-to-many forest plot |
| format_aries_mqtl | Get data from methylation QTL results |
| format_d | Format the returned table from the MySQL database |
| format_data | Read exposure or outcome data |
| format_gtex_eqtl | Get data from eQTL catalog into correct format |
| format_gwas_catalog | Get data selected from GWAS catalog into correct format |
| format_metab_qtls | Get data from metabolomic QTL results |
| format_mr_results | Format MR results for forest plot |
| format_proteomic_qtls | Get data from proteomic QTL results |
| generate_odds_ratios | Generate odds ratios |
| get_p_from_r2n | Calculate p-value from R-squared and sample size |
| get_population_allele_frequency | Estimate the allele frequency in population from case/control... |
| get_r_from_bsen | Estimate R-squared from beta, standard error and sample size |
| get_r_from_lor | Estimate proportion of variance of liability explained by SNP... |
| get_r_from_pn | Calculate variance explained from p-values and sample size |
| get_se | Get SE from effect size and p-value |
| harmonise_data | Harmonise the alleles and effects between the exposure and... |
| harmonise_ld_dat | Harmonise LD matrix against summary data |
| Isq | I-squared calculation |
| knit_report | Knit report using working environment |
| ld_matrix | Get LD matrix for list of SNPs |
| ldsc_h2 | Univariate LDSC |
| ldsc_h2_internal | Univariate LDSC |
| ldsc_rg | Bivariate LDSC |
| ldsc_rg_internal | Bivariate LDSC |
| make_dat | Convenient function to create a harmonised dataset |
| mr | Perform all Mendelian randomization tests |
| mr_density_plot | Density plot |
| mr_egger_regression | Egger's regression for Mendelian randomization |
| mr_egger_regression_bootstrap | Run bootstrap to generate standard errors for MR |
| mr_forest_plot | Forest plot |
| mr_forest_plot_grouped | Grouped forest plot |
| mr_funnel_plot | Funnel plot |
| mr_heterogeneity | Get heterogeneity statistics |
| mr_ivw | Inverse variance weighted regression |
| mr_ivw_fe | Inverse variance weighted regression (fixed effects) |
| mr_ivw_mre | Inverse variance weighted regression (multiplicative random... |
| mr_ivw_radial | Radial IVW analysis |
| mr_leaveoneout | Leave one out sensitivity analysis |
| mr_leaveoneout_plot | Plot results from leaveoneout analysis |
| mr_median | MR median estimators |
| mr_meta_fixed | Perform 2 sample IV using fixed effects meta analysis and... |
| mr_meta_fixed_simple | Perform 2 sample IV using simple standard error |
| mr_meta_random | Perform 2 sample IV using random effects meta analysis and... |
| mr_method_list | Get list of available MR methods |
| mr_mode | MR mode estimators |
| mr_moe | Mixture of experts |
| mr_penalised_weighted_median | Penalised weighted median MR |
| mr_pleiotropy_test | Test for horizontal pleiotropy in MR analysis |
| mr_raps | Robust adjusted profile score |
| mr_report | Generate MR report |
| mr_rucker | MR Rucker framework |
| mr_rucker_bootstrap | Run rucker with bootstrap estimates |
| mr_rucker_cooksdistance | MR Rucker with outliers automatically detected and removed |
| mr_rucker_jackknife | Run rucker with jackknife estimates |
| mr_scatter_plot | Create scatter plot with lines showing the causal estimate... |
| mr_sign | MR sign test |
| mr_simple_median | Simple median method |
| mr_simple_mode | MR simple mode estimator |
| mr_simple_mode_nome | MR simple mode estimator (NOME) |
| mr_singlesnp | Perform 2 sample MR on each SNP individually |
| mr_steiger | MR Steiger test of directionality |
| mr_steiger2 | MR Steiger test of directionality |
| mr_two_sample_ml | Maximum likelihood MR method |
| mr_uwr | Unweighted regression |
| mr_wald_ratio | Perform 2 sample IV using Wald ratio. |
| mr_weighted_median | Weighted median method |
| mr_weighted_mode | MR weighted mode estimator |
| mr_weighted_mode_nome | MR weighted mode estimator (NOME) |
| mr_wrapper | Perform full set of MR analyses |
| mv_basic | Perform basic multivariable MR |
| mv_extract_exposures | Extract exposure variables for multivariable MR |
| mv_extract_exposures_local | Attempt to perform MVMR using local data |
| mv_harmonise_data | Harmonise exposure and outcome for multivariable MR |
| mv_ivw | Perform IVW multivariable MR |
| mv_lasso_feature_selection | Apply LASSO feature selection to mvdat object |
| mv_multiple | Perform IVW multivariable MR |
| mv_residual | Perform basic multivariable MR |
| mv_subset | Perform multivariable MR on subset of features |
| pipe | Pipe operator |
| power_prune | Power prune |
| read_exposure_data | Read exposure data |
| read_outcome_data | Read outcome data |
| run_mrmix | Perform MRMix analysis on harmonised dat object |
| run_mr_presso | Wrapper for MR-PRESSO |
| simple_cap | Simple attempt at correcting string case |
| size.prune | Size prune |
| sort_1_to_many | Sort results for 1-to-many forest plot |
| split_exposure | Split exposure column |
| split_outcome | Split outcome column |
| standardise_units | Try to standardise continuous traits to be in standard... |
| steiger_filtering | Steiger filtering function |
| steiger_sensitivity | Evaluate the Steiger test's sensitivity to measurement error |
| subset_on_method | Subset MR-results on method |
| trim | Trim function to remove leading and trailing blank spaces |
| TwoSampleMR-package | TwoSampleMR: Two Sample MR Functions and Interface to MR Base... |
| weighted_median | Weighted median method |
| weighted_median_bootstrap | Calculate standard errors for weighted median method using... |
