Man pages for MRCIEU/TwoSampleMR
Two Sample MR functions and interface to MR Base database

allele_frequencyEstimate allele frequency from SNP
available_outcomesGet list of studies with available GWAS summary statistics...
available_outcomes_mysqlGet list of studies with available GWAS summary statistics
check_mrbase_accessCheck MR Base access level
check_passwordCheck password for MR Base API
cleanup_outcome_dataAvoid issues in MR by finding impossible vals and setting to...
clump_dataPerform LD clumping on SNP data
combine_all_mrresultsCombine all mr results
combine_dataCombine data
contingencyObtain 2x2 contingency table from marginal parameters and...
convert_outcome_to_exposureConvert outcome format to exposure format
create_labelCreate fixed width label
dat_to_MRInputConvert TwoSampleMR format to MendelianRandomization format
dat_to_RadialMRConvert dat to RadialMR format
default_parametersList of parameters for use with MR functions
directionality_testPerform MR Steiger test of directionality
enrichmentPerform enrichment analysis
enrichment_method_listGet list of available p-value enrichment methods
estimate_trait_sdEstimate trait SD by obtaining beta estimates from z-scores...
extract_instrumentsFind instruments for use in MR from the MR Base database
extract_outcome_dataSupply the output from 'read_exposure_data' and all the SNPs...
extract_outcome_data2Supply the output from 'read_exposure_data' and all the SNPs...
extract_outcome_data_mysqlExtract SNP effects from GWAS summary statistics
extract_outcome_data_using_getSupply the output from 'read_exposure_data' and all the SNPs...
fishers_combined_testFisher's combined test
forest_plotForest plot for multiple exposures and multiple outcomes
forest_plot_1_to_many1-to-many forest plot
forest_plot_basicA basic forest plot
forest_plot_basic2A basic forest plot
format_1_to_manyFormat MR results for a 1-to-many forest plot
format_aries_mqtlGet data from methylation QTL results
format_dFormat the returned table from the MySQL database
format_dataRead exposure or outcome data
format_gtex_eqtlGet data from eQTL catalog into correct format
format_gwas_catalogGet data selected from GWAS catalog into correct format
format_metab_qtlsGet data from metabolomic QTL results
format_mr_resultsFormat MR results for forest plot
format_proteomic_qtlsGet data from proteomic QTL results
generate_odds_ratiosGenerate odds ratios
get_mrbase_access_tokenGet access token for OAuth2 access to MR Base
get_mrbase_statusGet number of studies in database
get_passwordGet password from either global options or argument
get_p_from_r2nCalculate p-value from rsq and sample size
get_population_allele_frequencyEstimate the allele frequency in population from case/control...
get_r_from_lorEstimate proportion of variance of liability explained by SNP...
get_r_from_pnCalculate variance explained from p vals and sample size
get_seGet SE from effect size and pval
harmonise_dataHarmonise the alleles and effects between the exposure and...
iosCalculate index of suspicion
IsqCalculate I-square
knit_reportKnit report using working environment
ld_matrixGet LD matrix for list of SNPs
ld_pruning_apiPerform clumping on the chosen SNPs using through API
logging_infoDetails of how access token logs are used
mrPerform all Mendelian randomization tests
mr_density_plotDensity plot
mr_egger_regressionEgger's regression for Mendelian randomization
mr_egger_regression_bootstrapRun bootstrap to generate standard errors for MR
mr_forest_plotForest plot
mr_forest_plot_groupedGrouped forest plot
mr_funnel_plotFunnel plot
mr_heterogeneityGet heterogeneity stats
mr_ivwInverse variance weighted regression
mr_ivw_feInverse variance weighted regression (fixed effects)
mr_ivw_mreInverse variance weighted regression (multiplicative random...
mr_ivw_radialRadial IVW analysis
mr_leaveoneoutLeave one out sensitivity analysis
mr_leaveoneout_plotPlot results from leaveoneout analysis
mr_medianMR median estimators
mr_meta_fixedPerform 2 sample IV using fixed effects meta analysis and...
mr_meta_fixed_simplePerform 2 sample IV using simple standard error
mr_meta_randomPerform 2 sample IV using random effects meta analysis and...
mr_method_listGet list of available MR methods 8
mr_modeMR mode estimators
mr_moeMixture of experts
mr_penalised_weighted_medianPenalised weighted median MR
mr_pleiotropy_testTest for horizontal pleiotropy in MR analysis
mr_rapsRobust adjusted profile score
mr_reportGenerate MR report
mr_ruckerMR Rucker framework
mr_rucker_bootstrapRun rucker with bootstrap estimates
mr_rucker_cooksdistanceMR Rucker with outliers automatically detected and removed
mr_rucker_jackknifeRun rucker with jackknife estimates
mr_scatter_plotCreate scatter plot with lines showing the causal estimate...
mr_signMR sign test
mr_simple_medianSimple median method
mr_simple_modeMR simple mode estimator
mr_simple_mode_nomeMR weighted mode estimator (NOME)
mr_singlesnpPerform 2 sample MR on each SNP individually
mr_steigerMR Steiger test of directionality
mr_steiger2MR Steiger test of directionality
mr_two_sample_mlMaximum likelihood MR method
mr_uwrUnweighted regression
mr_wald_ratioPerform 2 sample IV using Wald ratio
mr_weighted_medianWeighted median method
mr_weighted_modeMR weighted mode estimator
mr_weighted_mode_nomeMR weighted mode estimator (NOME)
mr_wrapperPerform full set of MR analyses
mv_basicPerform basic multivariable MR
mv_extract_exposuresExtract exposure variables for multivariable MR
mv_harmonise_dataHarmonise exposure and outcome for multivariable MR
mv_ivwPerform IVW multivariable MR
mv_lasso_feature_selectionApply LASSO feature selection to mvdat object
mv_multiplePerform IVW multivariable MR
mv_residualPerform basic multivariable MR
mv_subsetPerform multivariable MR on subset of features
power_prunePower prune
read_exposure_dataRead exposure data
read_outcome_dataRead outcome data
revoke_mrbase_access_tokenRevoke access token for MR Base
run_mrPerform Rucker, Median and Mode
run_mr_pressoWrapper for MR-PRESSO
set_passwordSet password as a global option
simple_capSimple attempt at correcting string case
size.pruneSize prune
sort_1_to_manySort results for 1-to-many forest plot
split_exposureSplit exposure column
split_outcomeSplit outcome column
standardise_unitsTry to standardise continuous traits to be in standard...
steiger_filteringSteiger filtering function
steiger_sensitivityEvaluate the Steiger test's sensitivity to measurement error
subset_on_methodSubset MR-results on method
toggle_apiToggle API address between development and release
toggle_devToggle API address between development and release
trimTrim function to remove leading and trailing blank spaces
upload_file_to_apiUpload a file using POST request through API
weighted_medianWeighted median method
weighted_median_bootstrapCalculate standard errors for weighted median method using...
MRCIEU/TwoSampleMR documentation built on Oct. 17, 2019, 7:50 a.m.