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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
mrlocus_0.0.26.zip(r-4.7)mrlocus_0.0.26.zip(r-4.6)mrlocus_0.0.26.zip(r-4.5)
mrlocus_0.0.26.tgz(r-4.6-x86_64)mrlocus_0.0.26.tgz(r-4.6-arm64)mrlocus_0.0.26.tgz(r-4.5-x86_64)mrlocus_0.0.26.tgz(r-4.5-arm64)
mrlocus_0.0.26.tar.gz(r-4.7-arm64)mrlocus_0.0.26.tar.gz(r-4.7-x86_64)mrlocus_0.0.26.tar.gz(r-4.6-arm64)mrlocus_0.0.26.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mrlocus/json (API)

# 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

2.78 score 1 stars 12 scripts 11 exports 49 dependencies

Last updated from:d3dd5068a1. Checks:11 NOTE, 1 OK, 1 FAIL. Indexed: no.

Target	Result	Time
linux-devel-arm64	NOTE	304
linux-devel-x86_64	NOTE	356
source / vignettes	OK	381
linux-release-arm64	NOTE	297
linux-release-x86_64	NOTE	291
macos-release-arm64	NOTE	169
macos-release-x86_64	NOTE	491
macos-oldrel-arm64	NOTE	169
macos-oldrel-x86_64	NOTE	437
windows-devel	NOTE	375
windows-release	NOTE	364
windows-oldrel	NOTE	349
wasm-release	FAIL	177

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

Dependencies:abind backports BH callr checkmate cli cpp11 desc distributional farver generics ggplot2 glue gridExtra gtable inline isoband labeling lifecycle loo magrittr MASS matrixStats numDeriv otel pillar pkgbuild pkgconfig posterior processx ps QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel rlang rstan rstantools S7 scales StanHeaders tensorA tibble utf8 vctrs viridisLite withr

MRLocus - estimation of gene-to-trait effects

Rendered frommrlocus.Rmdusingknitr::rmarkdown

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