INTACT

DOI: 10.18129/B9.bioc.INTACT  

Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis

Bioconductor version: Release (3.17)

This package integrates colocalization probabilities from colocalization analysis with transcriptome-wide association study (TWAS) scan summary statistics to implicate genes that may be biologically relevant to a complex trait. The probabilistic framework implemented in this package constrains the TWAS scan z-score-based likelihood using a gene-level colocalization probability. Given gene set annotations, this package can estimate gene set enrichment using posterior probabilities from the TWAS-colocalization integration step.

Author: Jeffrey Okamoto [aut, cre] , Xiaoquan Wen [aut]

Maintainer: Jeffrey Okamoto <jokamoto at umich.edu>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("INTACT")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("INTACT")

 

HTML	R Script	INTACT: Integrate TWAS and Colocalization Analysis for Gene Set Enrichment
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bayesian, GeneSetEnrichment, Software
Version	1.0.2
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	GPL-3 + file LICENSE
Depends	R (>= 4.2.0)
Imports	SQUAREM, bdsmatrix, numDeriv, stats
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/jokamoto97/INTACT
BugReports	https://github.com/jokamoto97/INTACT/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	INTACT_1.0.2.tar.gz
Windows Binary	INTACT_1.0.2.zip
macOS Binary (x86_64)	INTACT_1.0.2.tgz
macOS Binary (arm64)	INTACT_1.0.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/INTACT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/INTACT
Bioc Package Browser	https://code.bioconductor.org/browse/INTACT/
Package Short Url	https://bioconductor.org/packages/INTACT/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive