finemappeR is an R package that utilizes torus and susieR to perform functionally-informed genetic finemapping.
We recommend using R > 3.5 (has not been tested on older versions).
The package depends on TORUS, an external C++ library. To ensure this package is compiled, your system must have the following C/C++ libraries are required for compiling the source code
- GNU GSL library
- Zlib library
- Boost C++ library
Begin by installing this repo:
devtools::install_github('aselewa/finemappeR')
After installing, check that it loads properly:
library(finemappeR)
Finemapping requires linkage-disequilibrium information. We utilize the R package bigsnpr to read in PLINK files (bed/bim/fam) into R on the fly. If you have PLINK files, you can use bigsnpr::snp_readBed() to obtain a file with .rds extension. This RDS file is used for downstream analyses when attached with bigsnpr::snp_attach().