Package: pleiotest 1.0.0

pleiotest: Fast Sequential Pleiotropy Test

It performs a fast multi-trait genome-wide association analysis based on seemingly unrelated regressions. It tests for pleiotropic effects based on a series of Intersection-Union Wald tests. The package can handle large and unbalanced data and plot results.

Authors:Fernando Aguate [aut, cre], Gustavo de los Campos [aut], Alexander Grueneberg [ctb]

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pleiotest.pdf |pleiotest.html✨
pleiotest/json (API)

# Install 'pleiotest' in R:

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

Bug tracker:https://github.com/feraguate/pleiotest/issues

Uses libs:

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

On CRAN:

openblas cpp

2.70 score 1 stars 2 scripts 140 downloads 9 exports 3 dependencies

Last updated 3 years agofrom:2cde7fb28a. Checks:1 OK, 11 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 31 2025
R-4.5-win-x86_64	NOTE	Mar 31 2025
R-4.5-mac-x86_64	NOTE	Mar 31 2025
R-4.5-mac-aarch64	NOTE	Mar 31 2025
R-4.5-linux-x86_64	NOTE	Mar 31 2025
R-4.4-win-x86_64	NOTE	Mar 31 2025
R-4.4-mac-x86_64	NOTE	Mar 31 2025
R-4.4-mac-aarch64	NOTE	Mar 31 2025
R-4.4-linux-x86_64	NOTE	Mar 31 2025
R-4.3-win-x86_64	NOTE	Mar 31 2025
R-4.3-mac-x86_64	NOTE	Mar 31 2025
R-4.3-mac-aarch64	NOTE	Mar 31 2025

Exports:identify_subsets manhattan_plot mt_gwas pleio_ideogram pleio_plot pleio_simulate pleio_test pleioR xrsx_xrsy

Dependencies:RColorBrewer Rcpp RcppArmadillo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Internal function to identify sub-sets of data and return a list with IDs.	identify_subsets
Single Trait Manhattan plot	manhattan_plot
Multi-trait Genome wide association model.	mt_gwas
Plot ideogram from pleio_test results	pleio_ideogram
Pleiotropic manhattan plot	pleio_plot
Create simulations	pleio_simulate
Sequential Wald test for pleiotropy	pleio_test
Fit a multi-trait model to test for genetic pleiotropy	pleioR
Calculate XRsX and XRsY	xrsx_xrsy