README.md

In kevinlkx/mapgen: Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

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

Data preparation

Prepare input data: GWAS summary statistics, LD information, etc.

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.

Functional 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.

Gene mapping

Infer causal genes at each locus based on fine-mapping result and genomic annotations.

PIP partitioning by annotation categories

Partitioning finemapping PIPs by annotation categories.

Making track plots

Making track plots of GWAS, finemapping, and annotation data using Gviz package.

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. Nat Commun. 2023 Aug 17;14(1):4999. doi: 10.1038/s41467-023-40505-5. PMID: 37591828; PMCID: PMC10435551.

kevinlkx/mapgen documentation built on March 31, 2024, 11:03 p.m.