get_genome_ref: Download genome ref

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

Download genome ref

Description

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", "piggback"),
  population = c("eur", "afr", "amr", "eas", "sas"),
  timeout = 60 * 5,
  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

## Not run: 
genome_ref_path <- MAGMA.Celltyping::get_genome_ref()

## End(Not run)

NathanSkene/MAGMA_Celltyping documentation built on Aug. 21, 2023, 8:55 a.m.