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# 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 ## 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 or if you have any questions.