orthogene: Interspecies gene mapping

#' Gene expression data: mouse
#'
#' @description
#' Mean pseudobulk single-cell RNA-seq gene expression matrix.
#'
#' Data originally comes from Zeisel et al., 2018 (Cell).
#'
#' @source \href{https://pubmed.ncbi.nlm.nih.gov/30096314/}{Publication}
#' \code{
#' ctd <- ewceData::ctd()
#' exp_mouse <- as(ctd[[1]]$mean_exp, "sparseMatrix")
#' usethis::use_data(exp_mouse, overwrite = TRUE)
#' }
#' @format sparse matrix
#' @usage data("exp_mouse")
"exp_mouse"


#' Transcript expression data: mouse
#'
#' @description
#' Mean pseudobulk single-cell RNA-seq Transcript expression matrix.
#'
#' Data originally comes from Zeisel et al., 2018 (Cell).
#'
#' @source \href{https://pubmed.ncbi.nlm.nih.gov/30096314/}{Publication}
#' \code{
#' data("exp_mouse")
#' mapped_genes <- map_genes(genes = rownames(exp_mouse)[seq(1,100)],
#'                           target = "ENST",
#'                           species = "mouse",
#'                           drop_na = FALSE)
#' exp_mouse_enst <- exp_mouse[mapped_genes$input,]
#' rownames(exp_mouse_enst) <- mapped_genes$target
#' all_nas <- orthogene:::find_all_nas(rownames(exp_mouse_enst))
#' exp_mouse_enst <- exp_mouse_enst[!all_nas,]
#' exp_mouse_enst <- phenomix::add_noise(exp_mouse_enst)
#' usethis::use_data(exp_mouse_enst, overwrite = TRUE)
#' }
#' @format sparse matrix
#' @usage data("exp_mouse_enst")
"exp_mouse_enst"







#' Reference organisms
#'
#' @description
#' Organism for which gene references are available via
#' \href{https://biit.cs.ut.ee/gprofiler/gost}{gProfiler}
#' \href{https://biit.cs.ut.ee/gprofiler/api/util/organisms_list}{API}.
#' Used as a backup if API is not available.
#' @source \href{https://biit.cs.ut.ee/gprofiler/gost}{gProfiler site}
#' @format \code{data.frame}
#' @source  
#' \code{
#' # NOTE!: Must run usethis::use_data for all internal data at once.
#' # otherwise, the prior internal data will be overwritten.
#' #### Internal data 1: gprofiler_namespace ####
#'  #### Manually-prepared CSV ####
#'  path <- "inst/extdata/gprofiler_namespace.csv.gz"
#'  gprofiler_namespace <- data.table::fread(path)  
#'  #### Internal data 2: gprofiler_orgs
#'  gprofiler_orgs <- orthogene:::get_orgdb_gprofiler(use_local=FALSE)
#'  #### Save ####
#'  usethis::use_data(gprofiler_orgs,gprofiler_namespace,
#'   overwrite = TRUE, internal=TRUE) 
#' } 
#' @name gprofiler_orgs
NULL


#' \link[gprofiler2]{gconvert} namespaces
#'
#' @description
#' Available namespaces used by link[gprofiler2]{gconvert}. 
#' @source \href{https://biit.cs.ut.ee/gprofiler/page/namespaces-list}{
#' gProfiler site}
#' @format \code{data.frame}
#' @source 
#' \code{
#'  #### Manually-prepared CSV ####
#'  path <- "inst/extdata/gprofiler_namespace.csv.gz"
#'  gprofiler_namespace <- data.table::fread(path)  
#' }
#' @name gprofiler_namespace
NULL