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INTACT

This is the development version of INTACT; for the stable release version, see INTACT.

Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("INTACT")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Bayesian, GeneSetEnrichment, Software
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3 + file LICENSE
Depends R (>= 4.2.0)
Imports SQUAREM, bdsmatrix, numDeriv, stats
System Requirements
URL https://github.com/jokamoto97/INTACT
Bug Reports https://github.com/jokamoto97/INTACT/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat
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Package Archives

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

Source Package INTACT_1.3.0.tar.gz
Windows Binary INTACT_1.3.0.zip
macOS Binary (x86_64) INTACT_1.3.0.tgz
macOS Binary (arm64) INTACT_1.3.0.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