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]>

# Install 'MendelianRandomization' in R:

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

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

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

On CRAN:

75 exports 1 stars 5.97 score 88 dependencies 1 dependents 88 mentions 940 scripts 3.6k downloads

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

Target	Result	Date
Doc / Vignettes	OK	Aug 21 2024
R-4.5-win-x86_64	WARNING	Aug 21 2024
R-4.5-linux-x86_64	WARNING	Aug 21 2024
R-4.4-win-x86_64	WARNING	Aug 21 2024
R-4.4-mac-x86_64	WARNING	Aug 21 2024
R-4.4-mac-aarch64	WARNING	Aug 21 2024
R-4.3-win-x86_64	WARNING	Jul 22 2024
R-4.3-mac-aarch64	WARNING	Jul 22 2024
R-4.3-mac-x86_64	WARNING	Jul 22 2024

Exports:BF_dist calc.rho calcium calciumse chdlodds chdloddsse ci_normal ci_t cML_estimate cML_estimate_random cML_SdTheta condFstat coursedata decimals egger.bounds extract.pheno.csv fastgluc fastglucse hdlc hdlcse het.weight invcov_mvmr ldlc ldlcse lipid_eaf lipid_effect lipid_other loglikelihood loglikelihoodcorrel loglikelihoodrhocorrel mbe_boot mbe_est model.prior mr_allmethods mr_cML mr_conmix mr_divw mr_egger mr_forest mr_funnel mr_hetpen mr_input mr_ivw mr_lasso mr_loo mr_maxlik mr_mbe mr_median mr_mvcML mr_mvegger mr_mvgmm mr_mvinput mr_mvivw mr_mvlasso mr_mvmedian mr_mvpcgmm mr_pcgmm mr_pivw mr_plot MVcML_SdTheta MVmr_cML MVmr_cML_DP penalised.weights penalised.weights.delta pheno_input phenoscanner pl r.weights r.weights.delta simpleCap trig trigse values weighted.median weighted.median.boot.se

Dependencies:arrangements askpass base64enc bslib cachem cli codetools colorspace cpp11 crosstalk curl data.table DEoptimR digest dplyr evaluate fansi farver fastmap fontawesome foreach fs generics ggplot2 glmnet glue gmp gtable highr htmltools htmlwidgets httr isoband iterators iterpc jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix MatrixModels memoise mgcv mime munsell nlme numDeriv openssl pillar pkgconfig plotly promises purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen rjson rlang rmarkdown robustbase sass scales shape SparseM stringi stringr survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

Mendelian randomization vignette

Olena Yavorska, Stephen Burgess

Rendered fromVignette_MR.Rmdusingknitr::rmarkdownon Aug 21 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Data on effect of calcium on fasting glucose (correlated variants)	calc.rho calcium calciumse fastgluc fastglucse
Estimate with Regular Likelihood	cML_estimate
Estimate with Regular Likelihood Using Multiple Random Start Points	cML_estimate_random
Standard Error of Estimated Theta	cML_SdTheta
DIVW Class	DIVW-class
Egger Class	Egger-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 Class	IVW-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 Class	MaxLik-class
Mendelian randomization estimation using all methods	mr_allmethods mr_allmethods,MRInput-method
Constrained maximum likelihood (cML) method	mr_cML mr_cML,MRInput-method
Contamination mixture method	mr_conmix mr_conmix,MRInput-method
Debiased inverse-variance weighted method	mr_divw mr_divw,MRInput-method
MR-Egger method	mr_egger mr_egger,MRInput-method
Draw a forest plot of causal estimates	mr_forest mr_forest,MRInput-method
Draw a funnel plot of variant-specific estimates	mr_funnel mr_funnel,MRInput-method
Heterogeneity-penalized method	mr_hetpen mr_hetpen,MRInput-method
Inputting and formatting data for use in causal estimation	mr_input
Inverse-variance weighted method	mr_ivw mr_ivw,MRInput-method
MR-Lasso method	mr_lasso mr_lasso,MRInput-method
Leave-one-out estimates	mr_loo mr_loo,MRInput-method
Maximum-likelihood method	mr_maxlik mr_maxlik,MRInput-method
Mode-based method of Hartwig	mr_mbe mr_mbe,MRInput-method
Median-based method	mr_median mr_median,MRInput-method
Multivariable constrained maximum likelihood method	mr_mvcML mr_mvcML,MRMVInput-method
Multivariable MR-Egger method	mr_mvegger mr_mvegger,MRMVInput-method
Multivariable generalized method of moments (GMM) method	mr_mvgmm mr_mvgmm,MRMVInput-method
Inputting and formatting data for use in causal estimation	mr_mvinput
Multivariable inverse-variance weighted method	mr_mvivw mr_mvivw,MRMVInput-method
Multivariable MR-Lasso method	mr_mvlasso mr_mvlasso,MRMVInput-method
Multivariable median-based method	mr_mvmedian mr_mvmedian,MRMVInput-method
Multivariable principal components generalized method of moments (PC-GMM) method	mr_mvpcgmm mr_mvpcgmm,MRMVInput-method
Univariable principal components generalized method of moments (PC-GMM) method	mr_pcgmm mr_pcgmm,MRInput-method
Penalized inverse-variance weighted method	mr_pivw mr_pivw,MRInput-method
Draw a scatter plot of the genetic associations and/or causal estimates	mr_plot mr_plot,MRAll-method mr_plot,MRInput-method mr_plot,MRMVInput-method
MRAll Class	MRAll-class
MRcML Class	MRcML-class
MRConMix Class	MRConMix-class
MRHetPen Class	MRHetPen-class
MRInput Class	MRInput-class
MRLasso class	MRLasso-class
MRMBE Class	MRMBE-class
MRMVInput Class	MRMVInput-class
Standard error estimate for MVMR-cML-BIC	MVcML_SdTheta
MVEgger Class	MVEgger-class
MVGMM Class	MVGMM-class
MVIVW Class	MVIVW-class
MRMVLasso class	MVLasso-class
MRMVMedian class	MVMedian-class
MVMRcML method with Data Perturbation	MVmr_cML
MVMRcML method with Data Perturbation	MVmr_cML_DP
MVMRcML Class	MVMRcML-class
MVPCGMM Class	MVPCGMM-class
PCGMM Class	PCGMM-class
Extract summarized data from PhenoScanner	pheno_input
PhenoScanner	phenoscanner
PIVW Class	PIVW-class
WeightedMedian Class	WeightedMedian-class