#' Example colocalization results
#'
#' Example colocalization results from running \link[catalogueR]{COLOC_run}.
#' on GWAS summary stats from all loci in
#' \href{https://doi.org/10.1016/S1474-4422(19)30320-5}{Nalls23andMe_2019}.
#' These results were published in
#' \href{https://pubmed.ncbi.nlm.nih.gov/34617105/}{
#' Schilder & Raj (Human Molecular Genetics, 2021)}
#'
#' @param full Download the non-filtered version of the colocalization results
#' (Default: \code{FALSE}).
#' @inheritParams echodata::get_data
#'
#' @source
#' \code{
#' ##### Subset results ####
#' # Pre-processing
#' gwas.qtl_paths <- eQTLcatalogue_example_queries()
#' coloc_QTLs <- COLOC_run(gwas.qtl_paths = gwas.qtl_paths,
#' nThread = 4,
#' top_snp_only = TRUE,
#' save_path = "~/Desktop/coloc_results.tsv.gz")
#' # Import pre-processed results
#' URL <- file.path("https://github.com/RajLabMSSM/catalogueR/raw/master",
#' "data/coloc_QTLs.rda")
#' tmp <- file.path(tempdir(),basename(URL))
#' download.file(URL, tmp)
#' piggyback::pb_upload(file = tmp,
#' repo = "RajLabMSSM/catalogueR")
#'
#'
#' ##### Full results ####
#' URL <- file.path("https://github.com/RajLabMSSM/catalogueR/raw/master",
#' "data/coloc_QTLs_full.rda")
#' tmp <- file.path(tempdir(),basename(URL))
#' download.file(URL, tmp)
#' piggyback::pb_upload(file = tmp,
#' repo = "RajLabMSSM/catalogueR")
#' }
#' @family coloc
#' @export
#' @importFrom downloadR load_rdata
#' @importFrom echodata get_data
#' @examples
#' coloc_QTLs <- catalogueR::COLOC_get_example_res()
COLOC_get_example_res <- function(save_dir = tempdir(),
full = FALSE) {
tmp <- echodata::get_data(
fname = if (full) "coloc_QTLs_full.rda" else "coloc_QTLs.rda",
repo = "RajLabMSSM/catalogueR",
save_dir = save_dir
)
obj <- downloadR::load_rdata(fileName = tmp)
return(obj)
}
#### Deprecation function #####
get_coloc_QTLs <- function(...){
.Deprecated("eQTLcatalogue_query")
eQTLcatalogue_query(...)
}
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