neurogenomics / MAGMA_Files_Public

Publicly shared SNP-to-gene mappings of GWAS generated by MAGMA.

MAGMA_Files_Public: README

Brian M. Schilder

Updated: Dec-22-2021

GWAS gene set files generated by Multi-marker Analysis of GenoMic Annotation (MAGMA) for use in downstream analyses (e.g. MAGMA_celltyping).

Usage

These files can be imported using MAGMA_celltyping::import_magma.

if(!require(remotes)) install.packages("remotes")
if(!require(MAGMA.celltyping)) remotes::install_github("neurogenomics/MAGMA_celltyping@bschilder_dev") 

#### Search the MAGMA_Files_Public database's metadata ####
meta <- MAGMA.Celltyping::magma_files_metadata
#### Import MAGMA files ####
magma_dirs <- MAGMA.Celltyping::import_magma_files(ids = c("ieu-a-298"))

Metadata report

---

Session Info

utils::sessionInfo()

## R version 4.1.0 (2021-05-18)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] compiler_4.1.0  magrittr_2.0.1  fastmap_1.1.0   tools_4.1.0    
##  [5] htmltools_0.5.2 yaml_2.2.1      stringi_1.7.6   rmarkdown_2.11 
##  [9] knitr_1.36      stringr_1.4.0   xfun_0.28       digest_0.6.29  
## [13] rlang_0.4.12    evaluate_0.14