get_genome_ref.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/get_genome_ref.R
\name{get_genome_ref}
\alias{get_genome_ref}
\title{Download genome ref}
\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{
\item{genome_ref_path}{If not \code{NULL} and file exists,
this file path will be returned.}

\item{storage_dir}{Where to store genome ref.}

\item{method}{Get reference genome data from the
\href{https://ctg.cncr.nl/software/MAGMA/ref_data/}{MAGMA server} (slow).}

\item{population}{Which population subset of the genome reference
to include.
\itemize{
\item{"eur" : }{European descent
(Default simply because this is currently
the most common GWAS subpopulation).}
\item{"afr" : }{African descent.}
\item{"amr" : }{Ad Mixed American descent.}
\item{"eas" : }{East Asian descent.}
\item{"sas" : }{South Asian descent.}
}}

\item{timeout}{Number seconds to wait before ending the download
(Default: 5 minutes).}

\item{verbose}{Print messages.}
}
\value{
Directory where the genome reference data is stored.
}
\description{
Download and decompress the genome reference needed to run
\link[MAGMA.Celltyping]{map_snps_to_genes},
If the file already exists, it will simply return the path.
}
\examples{
\dontrun{
genome_ref_path <- MAGMA.Celltyping::get_genome_ref()
}
}