Package: GPA 1.19.0

Dongjun Chung

GPA: GPA (Genetic analysis incorporating Pleiotropy and Annotation)

This package provides functions for fitting GPA, a statistical framework to prioritize GWAS results by integrating pleiotropy information and annotation data. In addition, it also includes ShinyGPA, an interactive visualization toolkit to investigate pleiotropic architecture.

Authors:Dongjun Chung, Emma Kortemeier, Carter Allen

GPA_1.19.0.tar.gz
GPA_1.19.0.zip(r-4.5)GPA_1.19.0.zip(r-4.4)GPA_1.19.0.zip(r-4.3)
GPA_1.19.0.tgz(r-4.4-x86_64)GPA_1.19.0.tgz(r-4.4-arm64)GPA_1.19.0.tgz(r-4.3-x86_64)GPA_1.19.0.tgz(r-4.3-arm64)
GPA_1.19.0.tar.gz(r-4.5-noble)GPA_1.19.0.tar.gz(r-4.4-noble)
GPA_1.19.0.tgz(r-4.4-emscripten)GPA_1.19.0.tgz(r-4.3-emscripten)
GPA.pdf |GPA.html✨
GPA/json (API)
NEWS

# Install 'GPA' in R:

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

Bug tracker:https://github.com/dongjunchung/gpa/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:GPA-1.19.0(bioc 3.21)GPA-1.18.0(bioc 3.20)

software statisticalmethod classification genomewideassociation snp genetics clustering multiplecomparison preprocessing geneexpression differentialexpression cpp

6.11 score 13 stars 7 scripts 139 downloads 260 mentions 12 exports 68 dependencies

Last updated 2 months agofrom:adab3a99be. Checks:OK: 3 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win-x86_64	OK	Nov 29 2024
R-4.5-linux-x86_64	OK	Nov 29 2024
R-4.4-win-x86_64	NOTE	Nov 29 2024
R-4.4-mac-x86_64	NOTE	Nov 29 2024
R-4.4-mac-aarch64	NOTE	Nov 29 2024
R-4.3-win-x86_64	NOTE	Nov 29 2024
R-4.3-mac-x86_64	NOTE	Nov 29 2024
R-4.3-mac-aarch64	NOTE	Nov 29 2024

Exports:assoc aTest cov estimates fdr fitAll GPA print pTest se shinyGPA show

Dependencies:base64enc bslib cachem cli cluster colorspace commonmark crayon crosstalk digest DT evaluate fansi farver fastmap fontawesome fs ggplot2 ggrepel glue gtable highr htmltools htmlwidgets httpuv isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme permute pillar pkgconfig plyr promises R6 rappdirs RColorBrewer Rcpp rlang rmarkdown sass scales shiny shinyBS sourcetools tibble tinytex utf8 vctrs vegan viridisLite withr xfun xtable yaml

GPA

Rendered fromGPA-example.Rnwusingutils::Sweaveon Nov 29 2024.

Last update: 2020-04-07
Started: 2020-02-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
GPA (Genetic analysis incorporating Pleiotropy and Annotation)	GPA-package
Association mapping	assoc assoc,GPA-method
Hypothesis testing for annotation enrichment	aTest
Fit GPA model for all possible pairs of GWAS datasets	fitAll
Fit GPA model	GPA
Class "GPA"	cov cov,GPA-method estimates estimates,GPA-method fdr fdr,GPA-method GPA-class print,GPA-method se se,GPA-method show,GPA-method
Hypothesis testing for pleiotropy	pTest
Run ShinyGPA app	shinyGPA