Package: MendelianRandomization 0.9.0

MendelianRandomization: Mendelian Randomization Package

Encodes several methods for performing Mendelian randomization analyses with summarized data. Summarized data on genetic associations with the exposure and with the outcome can be obtained from large consortia. These data can be used for obtaining causal estimates using instrumental variable methods.

Authors:Olena Yavorska <[email protected]> James Staley <[email protected]>

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MendelianRandomization.pdf |MendelianRandomization.html✨
MendelianRandomization/json (API)
NEWS

# Install 'MendelianRandomization' in R:
install.packages('MendelianRandomization', repos = c('https://sb452.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sb452/mendelianrandomization/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

On CRAN:

6.94 score 1 stars 1 packages 928 scripts 3.1k downloads 88 mentions 75 exports 88 dependencies

Last updated 1 years agofrom:7c5864084e. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-win-x86_64WARNINGNov 01 2024
R-4.5-linux-x86_64WARNINGNov 01 2024
R-4.4-win-x86_64WARNINGNov 01 2024
R-4.4-mac-x86_64WARNINGNov 01 2024
R-4.4-mac-aarch64WARNINGNov 01 2024
R-4.3-win-x86_64WARNINGNov 01 2024
R-4.3-mac-x86_64WARNINGNov 01 2024
R-4.3-mac-aarch64WARNINGNov 01 2024

Exports:BF_distcalc.rhocalciumcalciumsechdloddschdloddsseci_normalci_tcML_estimatecML_estimate_randomcML_SdThetacondFstatcoursedatadecimalsegger.boundsextract.pheno.csvfastglucfastglucsehdlchdlcsehet.weightinvcov_mvmrldlcldlcselipid_eaflipid_effectlipid_otherloglikelihoodloglikelihoodcorrelloglikelihoodrhocorrelmbe_bootmbe_estmodel.priormr_allmethodsmr_cMLmr_conmixmr_divwmr_eggermr_forestmr_funnelmr_hetpenmr_inputmr_ivwmr_lassomr_loomr_maxlikmr_mbemr_medianmr_mvcMLmr_mveggermr_mvgmmmr_mvinputmr_mvivwmr_mvlassomr_mvmedianmr_mvpcgmmmr_pcgmmmr_pivwmr_plotMVcML_SdThetaMVmr_cMLMVmr_cML_DPpenalised.weightspenalised.weights.deltapheno_inputphenoscannerplr.weightsr.weights.deltasimpleCaptrigtrigsevaluesweighted.medianweighted.median.boot.se

Dependencies:arrangementsaskpassbase64encbslibcachemclicodetoolscolorspacecpp11crosstalkcurldata.tableDEoptimRdigestdplyrevaluatefansifarverfastmapfontawesomeforeachfsgenericsggplot2glmnetgluegmpgtablehighrhtmltoolshtmlwidgetshttrisobanditeratorsiterpcjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixModelsmemoisemgcvmimemunsellnlmenumDerivopensslpillarpkgconfigplotlypromisespurrrquantregR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrjsonrlangrmarkdownrobustbasesassscalesshapeSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Mendelian randomization vignette

Olena Yavorska, Stephen Burgess

Rendered fromVignette_MR.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2020-08-11
Started: 2016-08-31

Readme and manuals

Help Manual

Help pageTopics
Data on effect of calcium on fasting glucose (correlated variants)calc.rho calcium calciumse fastgluc fastglucse
Estimate with Regular LikelihoodcML_estimate
Estimate with Regular Likelihood Using Multiple Random Start PointscML_estimate_random
Standard Error of Estimated ThetacML_SdTheta
DIVW ClassDIVW-class
Egger ClassEgger-class
Extract summarized data from a PhenoScanner .csv file (legacy)extract.pheno.csv
Generate the list of inverse of covariance matrices used in 'MVMR-cML-DP'invcov_mvmr
IVW ClassIVW-class
Data on lipid effects on coronary artery disease (uncorrelated variants)chdlodds chdloddsse hdlc hdlcse ldlc ldlcse lipid_eaf lipid_effect lipid_other trig trigse
MaxLik ClassMaxLik-class
Mendelian randomization estimation using all methodsmr_allmethods mr_allmethods,MRInput-method
Constrained maximum likelihood (cML) methodmr_cML mr_cML,MRInput-method
Contamination mixture methodmr_conmix mr_conmix,MRInput-method
Debiased inverse-variance weighted methodmr_divw mr_divw,MRInput-method
MR-Egger methodmr_egger mr_egger,MRInput-method
Draw a forest plot of causal estimatesmr_forest mr_forest,MRInput-method
Draw a funnel plot of variant-specific estimatesmr_funnel mr_funnel,MRInput-method
Heterogeneity-penalized methodmr_hetpen mr_hetpen,MRInput-method
Inputting and formatting data for use in causal estimationmr_input
Inverse-variance weighted methodmr_ivw mr_ivw,MRInput-method
MR-Lasso methodmr_lasso mr_lasso,MRInput-method
Leave-one-out estimatesmr_loo mr_loo,MRInput-method
Maximum-likelihood methodmr_maxlik mr_maxlik,MRInput-method
Mode-based method of Hartwigmr_mbe mr_mbe,MRInput-method
Median-based methodmr_median mr_median,MRInput-method
Multivariable constrained maximum likelihood methodmr_mvcML mr_mvcML,MRMVInput-method
Multivariable MR-Egger methodmr_mvegger mr_mvegger,MRMVInput-method
Multivariable generalized method of moments (GMM) methodmr_mvgmm mr_mvgmm,MRMVInput-method
Inputting and formatting data for use in causal estimationmr_mvinput
Multivariable inverse-variance weighted methodmr_mvivw mr_mvivw,MRMVInput-method
Multivariable MR-Lasso methodmr_mvlasso mr_mvlasso,MRMVInput-method
Multivariable median-based methodmr_mvmedian mr_mvmedian,MRMVInput-method
Multivariable principal components generalized method of moments (PC-GMM) methodmr_mvpcgmm mr_mvpcgmm,MRMVInput-method
Univariable principal components generalized method of moments (PC-GMM) methodmr_pcgmm mr_pcgmm,MRInput-method
Penalized inverse-variance weighted methodmr_pivw mr_pivw,MRInput-method
Draw a scatter plot of the genetic associations and/or causal estimatesmr_plot mr_plot,MRAll-method mr_plot,MRInput-method mr_plot,MRMVInput-method
MRAll ClassMRAll-class
MRcML ClassMRcML-class
MRConMix ClassMRConMix-class
MRHetPen ClassMRHetPen-class
MRInput ClassMRInput-class
MRLasso classMRLasso-class
MRMBE ClassMRMBE-class
MRMVInput ClassMRMVInput-class
Standard error estimate for MVMR-cML-BICMVcML_SdTheta
MVEgger ClassMVEgger-class
MVGMM ClassMVGMM-class
MVIVW ClassMVIVW-class
MRMVLasso classMVLasso-class
MRMVMedian classMVMedian-class
MVMRcML method with Data PerturbationMVmr_cML
MVMRcML method with Data PerturbationMVmr_cML_DP
MVMRcML ClassMVMRcML-class
MVPCGMM ClassMVPCGMM-class
PCGMM ClassPCGMM-class
Extract summarized data from PhenoScannerpheno_input
PhenoScannerphenoscanner
PIVW ClassPIVW-class
WeightedMedian ClassWeightedMedian-class