MendelianRandomization: Mendelian Randomization Package

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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.

Author
Olena Yavorska <yavorsko@tcd.ie>
Date of publication
2016-09-30 23:09:43
Maintainer
Stephen Burgess <sb452@medschl.cam.ac.uk>
License
GPL-2 | GPL-3
Version
0.2.0

View on CRAN

Man pages

calcium
Data on effect of calcium on fasting glucose (correlated...
ci_normal
Calculate confidence intervals using the normal distribution
ci_t
Calculate confidence intervals using the t-distribution
coursedata
Course data
decimals
Produce nicely rounded numbers
egger.bounds
Calculates confidence intervals for the MR-Egger method
Egger-class
Egger Class
extract.pheno.csv
Extract summarized data from a PhenoScanner .csv file
getter
Applies method $ to different classes
IVW-class
IVW Class
ldlc
Data on lipid effects on coronary artery disease...
loglikelihood
Calculates log-likelihood with uncorrelated variants in...
loglikelihoodcorrel
Calculates log-likelihood with correlated variants in...
loglikelihoodrhocorrel
Calculates log-likelihood with correlation from sample...
MaxLik-class
MaxLik Class
MRAll-class
MRAll Class
mr_allmethods
Mendelian randomization estimation using all methods
mr_egger
MR-Egger method
mr_input
Inputting and formatting data for use in causal estimation
MRInput-class
MRInput Class
mr_ivw
Inverse-variance weighted method
mr_maxlik
Maximum-likelihood method
mr_median
Median-based method
mr_plot
Draw a scatter plot of the genetic associations and/or causal...
penalised.weights
Calculates p-values for penalization of weights
penalised.weights.delta
Calculates p-values for penalization of weights with...
r.weights
Calculates p-values for penalization of weights
r.weights.delta
Calculates p-values for penalization of weights with...
simpleCap
Capitalize a word
values
Applies method values() to different output classes
weighted.median
Weighted median function
weighted.median.boot.se
Weighted median standard error function
WeightedMedian-class
WeightedMedian Class

Files in this package

MendelianRandomization
MendelianRandomization/inst
MendelianRandomization/inst/extdata
MendelianRandomization/inst/extdata/vitD_snps_PhenoScanner_proxies.csv
MendelianRandomization/inst/extdata/vitD_snps_PhenoScanner.csv
MendelianRandomization/inst/doc
MendelianRandomization/inst/doc/Vignette_MR.R
MendelianRandomization/inst/doc/Vignette_MR.pdf
MendelianRandomization/inst/doc/Vignette_MR.Rmd
MendelianRandomization/NAMESPACE
MendelianRandomization/NEWS
MendelianRandomization/R
MendelianRandomization/R/AllClasses.R
MendelianRandomization/R/AllGenerics.R
MendelianRandomization/R/show-methods.R
MendelianRandomization/R/values-methods.R
MendelianRandomization/R/mr_allmethods-methods.R
MendelianRandomization/R/mr_ivw-methods.R
MendelianRandomization/R/AllData.R
MendelianRandomization/R/mr_median-methods.R
MendelianRandomization/R/mr_maxlik-methods.R
MendelianRandomization/R/extract.pheno.csv-function.R
MendelianRandomization/R/getter-methods.R
MendelianRandomization/R/mr_plot-methods.R
MendelianRandomization/R/1Data.R
MendelianRandomization/R/ExtraFunctions.R
MendelianRandomization/R/mr_egger-methods.R
MendelianRandomization/R/new-methods.R
MendelianRandomization/vignettes
MendelianRandomization/vignettes/Vignette_MR.html
MendelianRandomization/vignettes/Vignette_MR.Rmd
MendelianRandomization/MD5
MendelianRandomization/build
MendelianRandomization/build/vignette.rds
MendelianRandomization/DESCRIPTION
MendelianRandomization/man
MendelianRandomization/man/mr_plot.Rd
MendelianRandomization/man/penalised.weights.delta.Rd
MendelianRandomization/man/ci_normal.Rd
MendelianRandomization/man/simpleCap.Rd
MendelianRandomization/man/loglikelihoodrhocorrel.Rd
MendelianRandomization/man/mr_egger.Rd
MendelianRandomization/man/loglikelihood.Rd
MendelianRandomization/man/mr_maxlik.Rd
MendelianRandomization/man/extract.pheno.csv.Rd
MendelianRandomization/man/values.Rd
MendelianRandomization/man/getter.Rd
MendelianRandomization/man/mr_input.Rd
MendelianRandomization/man/ldlc.Rd
MendelianRandomization/man/r.weights.delta.Rd
MendelianRandomization/man/coursedata.Rd
MendelianRandomization/man/Egger-class.Rd
MendelianRandomization/man/ci_t.Rd
MendelianRandomization/man/penalised.weights.Rd
MendelianRandomization/man/MaxLik-class.Rd
MendelianRandomization/man/r.weights.Rd
MendelianRandomization/man/MRInput-class.Rd
MendelianRandomization/man/mr_allmethods.Rd
MendelianRandomization/man/decimals.Rd
MendelianRandomization/man/calcium.Rd
MendelianRandomization/man/loglikelihoodcorrel.Rd
MendelianRandomization/man/mr_median.Rd
MendelianRandomization/man/weighted.median.boot.se.Rd
MendelianRandomization/man/IVW-class.Rd
MendelianRandomization/man/egger.bounds.Rd
MendelianRandomization/man/WeightedMedian-class.Rd
MendelianRandomization/man/mr_ivw.Rd
MendelianRandomization/man/weighted.median.Rd
MendelianRandomization/man/MRAll-class.Rd