Mapgen

Mapgen is a multi-function software that performs the following tasks:

1. Enrichment analysis of functional annotations for a trait of interest.
2. Functionally-informed genetic fine-mapping.
3. Gene mapping based on fine-mapping result and genomic annotations.

Installation

You can install the development version of mapgen from GitHub with:

install.packages("remotes")
remotes::install_github("xinhe-lab/mapgen")

After installing, check that it loads properly:

library(mapgen)

Tutorials

1. Data preparation

Prepare input data: GWAS summary statistics, LD reference panel, etc.

2. Enrichment analysis

Assess the enrichment of genetic signals of a trait of interest in functional annotations using TORUS.

*Please install TORUS software package, if you need to run enrichment analysis.

3. Fine-mapping

Perform Bayesian statistical fine-mapping using SuSiE on trait-associated loci, using a informative prior that favors variants located in enriched annotations.

*Please install susieR package, if you need to run fine-mapping with GWAS summary statistics.

4. Gene mapping

Infer causal genes at each locus based on fine-mapping result and genomic annotations, including gene annotations, chromatin loops, etc.

Reference

Alan Selewa*, Kaixuan Luo*, Michael Wasney, Linsin Smith, Xiaotong Sun, Chenwei Tang, Heather Eckart, Ivan Moskowitz, Anindita Basu, Xin He, Sebastian Pott. Single-cell genomics improves the discovery of risk variants and genes of Atrial Fibrillation. medRxiv 2022.02.02.22270312; doi: https://doi.org/10.1101/2022.02.02.22270312