Bioconductor – INTACT (development version)

DOI: 10.18129/B9.bioc.INTACT  

This is the development version of INTACT; to use it, please install the devel version of Bioconductor.

Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis

Bioconductor version: Development (3.17)

This package integrates colocalization probabilites 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
“4.3”) 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")

 

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INTACT: Integrate TWAS and Colocalization Analysis for Gene Set Enrichment
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