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")
INTACT: Integrate TWAS and Colocalization Analysis for Gene Set Enrichment | ||
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
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