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Download genome ref

Source: R/get_genome_ref.R
get_genome_ref.Rd

Download and decompress the genome reference needed to run map_snps_to_genes, If the file already exists, it will simply return the path.

Usage

get_genome_ref(
  genome_ref_path = NULL,
  storage_dir = tools::R_user_dir("MAGMA.Celltyping", which = "cache"),
  method = c("magma"),
  population = c("eur", "afr", "amr", "eas", "sas"),
  timeout = 60 * 15,
  verbose = TRUE
)

Arguments

genome_ref_path

If not NULL and file exists, this file path will be returned.

storage_dir

Where to store genome ref.

method

Get reference genome data from the MAGMA server (slow).

population

Which population subset of the genome reference to include.

  • "eur" : European descent (Default simply because this is currently the most common GWAS subpopulation).

  • "afr" : African descent.

  • "amr" : Ad Mixed American descent.

  • "eas" : East Asian descent.

  • "sas" : South Asian descent.

timeout

Number seconds to wait before ending the download (Default: 5 minutes).

verbose

Print messages.

Value

Directory where the genome reference data is stored.

Examples

if (FALSE) { # \dontrun{
genome_ref_path <- get_genome_ref()
} # }