Package: GPA 1.25.0

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_1.25.0.tar.gz
GPA_1.25.0.zip(r-4.7)GPA_1.25.0.zip(r-4.6)GPA_1.25.0.zip(r-4.5)
GPA_1.25.0.tgz(r-4.6-x86_64)GPA_1.25.0.tgz(r-4.6-arm64)GPA_1.25.0.tgz(r-4.5-x86_64)GPA_1.25.0.tgz(r-4.5-arm64)
GPA_1.25.0.tar.gz(r-4.7-arm64)GPA_1.25.0.tar.gz(r-4.7-x86_64)GPA_1.25.0.tar.gz(r-4.6-arm64)GPA_1.25.0.tar.gz(r-4.6-x86_64)
GPA_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GPA/json (API)

# 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-1.25.0(bioc 3.24)GPA-1.24.0(bioc 3.23)

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

6.32 score 16 stars 13 scripts 260 mentions 12 exports 63 dependencies

Last updated from:f20fe5cf99. Checks:1 ERROR, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	171
linux-devel-arm64	OK	180
linux-devel-x86_64	OK	233
source / vignettes	OK	278
linux-release-arm64	OK	178
linux-release-x86_64	OK	189
macos-release-arm64	OK	100
macos-release-x86_64	OK	262
macos-oldrel-arm64	OK	98
macos-oldrel-x86_64	OK	220
windows-devel	OK	142
windows-release	OK	138
windows-oldrel	OK	132
wasm-release	OK	172

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

Dependencies:base64enc bslib cachem cli cluster commonmark cpp11 crosstalk digest DT evaluate 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 nlme otel permute plyr promises R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S7 sass scales shiny shinyBS sourcetools tinytex vctrs vegan viridisLite withr xfun xtable yaml

GPA

Rendered fromGPA-example.Rnwusingutils::Sweave

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