INTACT

This is the released version of INTACT; for the devel version, see INTACT.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17

Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis

Bioconductor version: Release (3.23)

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] ORCID: 0000-0001-9988-1618 , Xiaoquan Wen [aut] ORCID: 0000-0001-8990-2737

Maintainer: Jeffrey Okamoto <jokamoto at umich.edu>

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

Jeffrey Okamoto, Xiaoquan Wen. INTACT: Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis. doi:10.18129/B9.bioc.INTACT, R package version 1.12.0, https://bioconductor.org/packages/INTACT.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, GeneSetEnrichment, Software
Version	1.12.0
In Bioconductor since	BioC 3.17 (R-4.3) (3.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.3.0)
Imports	SQUAREM, bdsmatrix, numDeriv, stats, tidyr, ggplot2
System Requirements
URL	https://github.com/jokamoto97/INTACT
Bug Reports	https://github.com/jokamoto97/INTACT/issues

Suggests	BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	INTACT_1.12.0.tar.gz
Windows Binary (x86_64)	INTACT_1.12.0.zip
macOS Binary (big-sur-x86_64)	INTACT_1.12.0.tgz
macOS Binary (sonoma-arm64)	INTACT_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/INTACT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/INTACT
Package Short Url	https://bioconductor.org/packages/INTACT/
Package Downloads Report	Download Stats