This is the development version of INTACT; for the stable release version, see INTACT.
Integrate TWAS and Colocalization Analysis for Gene Set Enrichment AnalysisBioconductor version: Development (3.22)
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, entercitation("INTACT")): Installation
To install this package, start R (version "4.5") 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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("INTACT")Follow Installation instructions to use this package in your R session.
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