# INTACT
INTACT (INtegration of TWAS And ColocalizaTion) is an R package for constraining
transcriptome-wide association study correlation statistics through an empirical
Bayes approach. As input, INTACT takes gene-level colocalization probabilities
and TWAS z-statistics, returning a posterior probability of putative causality
for each gene.
The package also performs gene set enrichment estimation using probabilistic
INTACT results and a list of pre-defined gene sets (INTACT-GSE).
For a thorough description of the methodology, refer to
https://doi.org/10.1016/j.ajhg.2022.12.002.
## Installing via Github
```
library(devtools)
devtools::install_github("jokamoto97/INTACT")
```
## Installing via Bioconductor
```
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("INTACT")
```
## Examples
Here is an example of how to integrate colocalization probabilities and TWAS
z-statistics for a simulated data set ```simdat```:
```
intact(GLCP_vec=simdat$GLCP, z_vec = simdat$TWAS_z)
```
To perform gene set enrichment analysis using ```simdat``` and pre-defined gene
set list ```gene_set_list```, run
```
intactGSE(gene_data = simdat, gene_sets = gene_set_list)
```
## Support
Please contact xwen@umich.edu or jokamoto@umich.edu if you have any questions.
