INTACT

This is the development version of INTACT; for the stable release 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: Development (3.24)

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 1.13.0, 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")

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, GeneSetEnrichment, Software
Version	1.13.0
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_1.13.0.tar.gz
Windows Binary (x86_64)	INTACT_1.13.0.zip
macOS Binary (big-sur-x86_64)	INTACT_1.13.0.tgz
macOS Binary (sonoma-arm64)	INTACT_1.13.0.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