Two Sample MR functions and interface to MR Base database

allele_frequency | Estimate allele frequency from SNP |

available_outcomes | Get list of studies with available GWAS summary statistics... |

available_outcomes_mysql | Get list of studies with available GWAS summary statistics |

check_mrbase_access | Check MR Base access level |

check_password | Check password for MR Base API |

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 format to exposure format |

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 |

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 SNPs... |

extract_outcome_data2 | Supply the output from 'read_exposure_data' and all the SNPs... |

extract_outcome_data_mysql | Extract SNP effects from GWAS summary statistics |

extract_outcome_data_using_get | Supply the output from 'read_exposure_data' and all the SNPs... |

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_mrbase_access_token | Get access token for OAuth2 access to MR Base |

get_mrbase_status | Get number of studies in database |

get_password | Get password from either global options or argument |

get_p_from_r2n | Calculate p-value from rsq and sample size |

get_population_allele_frequency | Estimate the allele frequency in population from case/control... |

get_r_from_lor | Estimate proportion of variance of liability explained by SNP... |

get_r_from_pn | Calculate variance explained from p vals and sample size |

get_se | Get SE from effect size and pval |

harmonise_data | Harmonise the alleles and effects between the exposure and... |

ios | Calculate index of suspicion |

Isq | Calculate I-square |

knit_report | Knit report using working environment |

ld_matrix | Get LD matrix for list of SNPs |

ld_pruning_api | Perform clumping on the chosen SNPs using through API |

logging_info | Details of how access token logs are used |

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 stats |

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 8 |

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 weighted 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_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 |

power_prune | Power prune |

read_exposure_data | Read exposure data |

read_outcome_data | Read outcome data |

revoke_mrbase_access_token | Revoke access token for MR Base |

run_mr | Perform Rucker, Median and Mode |

run_mr_presso | Wrapper for MR-PRESSO |

set_password | Set password as a global option |

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 |

toggle_api | Toggle API address between development and release |

toggle_dev | Toggle API address between development and release |

trim | Trim function to remove leading and trailing blank spaces |

upload_file_to_api | Upload a file using POST request through API |

weighted_median | Weighted median method |

weighted_median_bootstrap | Calculate standard errors for weighted median method using... |

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