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Package: mrlocus 0.0.26

Michael Love

mrlocus: MRLocus - Mendelian Randomization per locus

Mendelian Randomization per locus, leveraging eQTL and GWAS summary statistics, for estimation of gene-to-trait effect size and dispersion.

Authors:Anqi Zhu [aut], Nana Matoba [aut], Jason Stein [aut], Michael Love [aut, cre]

mrlocus_0.0.26.tar.gz
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mrlocus_0.0.26.tgz(r-4.4-x86_64)mrlocus_0.0.26.tgz(r-4.4-arm64)mrlocus_0.0.26.tgz(r-4.3-x86_64)mrlocus_0.0.26.tgz(r-4.3-arm64)
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mrlocus.pdf |mrlocus.html✨
mrlocus/json (API)
NEWS

# Install 'mrlocus' in R:

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

Bug tracker:https://github.com/thelovelab/mrlocus/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

2.70 score 1 stars 9 scripts 11 exports 53 dependencies

Last updated 1 years agofrom:d3dd5068a1. Checks:OK: 1 NOTE: 8. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 25 2024
R-4.5-win-x86_64	NOTE	Nov 25 2024
R-4.5-linux-x86_64	NOTE	Nov 25 2024
R-4.4-win-x86_64	NOTE	Nov 25 2024
R-4.4-mac-x86_64	NOTE	Nov 25 2024
R-4.4-mac-aarch64	NOTE	Nov 25 2024
R-4.3-win-x86_64	NOTE	Nov 25 2024
R-4.3-mac-x86_64	NOTE	Nov 25 2024
R-4.3-mac-aarch64	NOTE	Nov 25 2024

Exports:collapseHighCorSNPs extractForSlope fitBetaColoc fitSlope flipAllelesAndGather makeSimDataForMrlocus normalizedAllelicSpread plotInitEstimates plotMrlocus priorCheck trimClusters

Dependencies:abind backports BH callr checkmate cli colorspace desc distributional fansi farver generics ggplot2 glue gridExtra gtable inline isoband labeling lattice lifecycle loo magrittr MASS Matrix matrixStats mgcv munsell nlme numDeriv pillar pkgbuild pkgconfig posterior processx ps QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel rlang rstan rstantools scales StanHeaders tensorA tibble utf8 vctrs viridisLite withr

MRLocus - estimation of gene-to-trait effects

Anqi Zhu, Nana Matoba, Jason Stein, Michael Love

Rendered frommrlocus.Rmdusingknitr::rmarkdownon Nov 25 2024.

Last update: 2023-08-16
Started: 2020-06-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
MRLocus - see this page for typical order of functions	mrlocus-package mrlocus
Collapse high correlation SNPs	collapseHighCorSNPs
Extract SNPs from colocalization for slope fitting	extractForSlope
Fit the colocalization model per signal cluster	fitBetaColoc
Fit the mediation slope model: effect of A on B	fitSlope
Flip alleles and gather results into lists	flipAllelesAndGather
Make simple simulated summary data	makeSimDataForMrlocus
Estimate the normalized allelic spread	normalizedAllelicSpread
Plot initial estimates over signal clusters	plotInitEstimates
Plot estimates from MRLocus slope fitting step	plotMrlocus
Basic prior checks on MRLocus slope fit	priorCheck
Trim signal clusters based on pairwise r2	trimClusters