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