#' Check species
#'
#' If species arguments are \code{NULL}, set default species.
#'
#' @param sctSpecies_origin_default Default value for \code{sctSpecies_origin}.
#' @inheritParams bootstrap_enrichment_test
#' @returns List of corrected species names.
#'
#' @keywords internal
check_species <- function(genelistSpecies = NULL,
sctSpecies = NULL,
sctSpecies_origin = NULL,
sctSpecies_origin_default="mouse",
verbose = TRUE) {
if (is.null(genelistSpecies)) {
messager(
"Warning: genelistSpecies not provided.",
"Setting to 'human' by default.",
v = verbose
)
genelistSpecies <- "human"
}
if (is.null(sctSpecies)) {
messager(
"Warning: sctSpecies not provided.",
"Setting to 'mouse' by default.",
v = verbose
)
sctSpecies <- "mouse"
}
if (is.null(sctSpecies_origin) &&
!is.null(sctSpecies_origin_default)) {
messager(
"Warning: sctSpecies_origin not provided.",
"Setting to",shQuote(sctSpecies_origin_default),
"by default.",
v = verbose
)
sctSpecies_origin <- sctSpecies_origin_default
}
return(list(
genelistSpecies = genelistSpecies,
sctSpecies = sctSpecies,
sctSpecies_origin = sctSpecies_origin
))
}
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