Skip to content
forked from xinhe-lab/mapgen

R package to perform gene mapping using functionally-informed genetic fine mapping

License

Unknown, MIT licenses found

Licenses found

Unknown
LICENSE
MIT
LICENSE.md
Notifications You must be signed in to change notification settings

kevinlkx/mapgen

 
 

Repository files navigation

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

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

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.

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.

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

Partitioning finemapping PIPs by annotation categories.

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.

About

R package to perform gene mapping using functionally-informed genetic fine mapping

Resources

License

Unknown, MIT licenses found

Licenses found

Unknown
LICENSE
MIT
LICENSE.md

Stars

Watchers

Forks

Packages

No packages published

Languages

  • R 100.0%