Import preprocessed MAGMA files — import_magma

Import preprocessed MAGMA SNPs-to-genes mapping files for many GWAS. These files were generated using map_snps_to_genes and are publicly available via the MAGMA_Files_Public GitHub repository. Metadata for each dataset (including trait descriptions) can be found here here.

import_magma_files(
  save_dir = tempdir(),
  ids = NULL,
  file_types = c(".genes.out", ".genes.raw"),
  overwrite = FALSE,
  return_dir = TRUE,
  return_tables = FALSE,
  nested = FALSE,
  nThread = 1,
  verbose = TRUE
)

Source

MAGMA_Files_Public GitHub repository

Arguments

save_dir: Parent folder where you want to save the MAGMA files.
ids: [Optional] OpenGWAS dataset IDs. You see metadata for the GWAS here.
file_types: MAGMA file types to import. Both ".genes.out" and ".genes.raw" are needed to run MAGMA.Celltyping cell-type enrichment functions
overwrite: If the files have already been downloaded in the specified directory, these downloads will be skipped. Set overwrite=TRUE to force them to be re-downloaded (Default: FALSE).
return_dir: Return a list of unique directory names instead of the full file paths (Default: TRUE).
return_tables: Returns the files imported as tables (TRUE), instead of as paths (default: FALSE). Overrides return_dir argument.
nested: Return files as a list nested by id (default: FALSE).
nThread: Number of threads to parallelise downloads across.
verbose: Print messages.

Value

Named vector of paths to downloaded MAGMA files (or directories), or a data.table.

Examples

magma_dirs <- MAGMA.Celltyping::import_magma_files(ids = c("ieu-a-298"))
#> Using built-in example files: ieu-a-298.tsv.gz.35UP.10DOWN
#> Returning MAGMA directories.