TisCoMM

TisCoMM leverages the co-regulation of genetic variations across different tissues explicitly via a unified probabilistic model. TisCoMM not only performs hypothesis testing to prioritize gene-trait associations black, but also detects the tissue-specific role of candidate target genes in complex traits. To make use of widely available GWAS summary statistics, we extend TisCoMM to use summary-level data, namely, TisCoMM-S$^2$.

TisCoMM R package implements the TisCoMM method described in Shi 2020. Get started with the User Manual.

Installation

To install the development version of TisCoMM, it's easiest to use the 'devtools' package. Note that TisCoMM depends on the 'Rcpp' package, which also requires appropriate setting of Rtools and Xcode for Windows and Mac OS/X, respectively.

library(devtools)
install_github("XingjieShi/TisCoMM")

Usage

library(TisCoMM)
?TisCoMM

Replicate simulation results in Shi et al. (2019)

All the simulation results can be reproduced by using the code in folder simulation. Before running simulation to reproduce the results, please familiarize yourself with TisCoMM using 'TisCoMM' vignette.

1. Simulation results for multi-tissue joint test can be reproduced by following steps:

   • ExampleOne.R: This function can be run in a HPC cluster (with minor revisions, it could be run on a PC), it will output files, named pvalue_hz0.1_hc0.25_rhoX5_s5_batch-6.txt, which contain inference results of each replicate, for all multi-tissue TWAS methods: TisCoMM, TisCoMM-S$^2$, MultiXcan, S-MultiXcan and UTMOST.

   • ExampleOnePlot.R: This function produces simulation figures of joint test in Shi et al. (2019).

2. Simulation results for tissue-specific test can be reproduced by following steps:

   • PartCoMMCOR.R: This function can be run in a HPC cluster (with minor revisions, it could be run on a PC), it will output files, named part_hc4_rhoX8_rhoW8nz_ti2_batch-2.rds, which contain inference results of each replicate, for all single-tissue TWAS methods: CoMM, PrediXcan, and TWAS.

   • SummaryCOR.R: This function produces simulation figures of tissue-specific test in Shi et al. (2019).

Reference

A tissue-specific collaborative mixed model for jointly analyzing multiple tissues in transcriptome-wide association studies