replace deprecated function

egeulgen · Feb 15, 2025 · dd17c7e · dd17c7e
1 parent 598d99a
commit dd17c7e
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/R/data_generation.R b/R/data_generation.R
@@ -236,7 +236,7 @@ get_reactome_gsets <- function() {
 #' Retrieve Organism-specific MSigDB Gene Sets
 #'
 #' @param species species name, such as Homo sapiens, Mus musculus, etc.
-#' See \code{\link[msigdbr]{msigdbr_show_species}} for all the species available in
+#' See \code{\link[msigdbr]{msigdbr_species}} for all the species available in
 #' the msigdbr package
 #' @param collection collection. i.e., H, C1, C2, C3, C4, C5, C6, C7.
 #' @param subcollection sub-collection, such as CGP, BP, etc. (default = NULL,
@@ -288,7 +288,7 @@ get_mgsigdb_gsets <- function(species = "Homo sapiens", collection, subcollectio
 #' @param org_code (Used for 'KEGG' only) KEGG organism code for the selected organism. For a full list
 #' of all available organisms, see \url{https://www.genome.jp/kegg/catalog/org_list.html}
 #' @param species (Used for 'MSigDB' only) species name, such as Homo sapiens, Mus musculus, etc.
-#' See \code{\link[msigdbr]{msigdbr_show_species}} for all the species available in
+#' See \code{\link[msigdbr]{msigdbr_species}} for all the species available in
 #' the msigdbr package (default = 'Homo sapiens')
 #' @param collection (Used for 'MSigDB' only) collection. i.e., H, C1, C2, C3, C4, C5, C6, C7.
 #' @param subcollection (Used for 'MSigDB' only)  sub-collection, such as CGP, MIR, BP, etc. (default = NULL,
@@ -299,7 +299,7 @@ get_mgsigdb_gsets <- function(species = "Homo sapiens", collection, subcollectio
 #' \item{descriptions - A named vector containing the descriptions for each gene set}
 #' }. For 'KEGG' and 'MSigDB', it is possible to choose a specific organism. For a full list
 #' of all available KEGG organisms, see \url{https://www.genome.jp/kegg/catalog/org_list.html}.
-#' See \code{\link[msigdbr]{msigdbr_show_species}} for all the species available in
+#' See \code{\link[msigdbr]{msigdbr_species}} for all the species available in
 #' the msigdbr package used for obtaining 'MSigDB' gene sets.
 #' For Reactome, there is only one collection of pathway gene sets.
 #' @export

diff --git a/man/get_gene_sets_list.Rd b/man/get_gene_sets_list.Rd
diff --git a/man/get_mgsigdb_gsets.Rd b/man/get_mgsigdb_gsets.Rd
diff --git a/vignettes/obtain_data.Rmd b/vignettes/obtain_data.Rmd
@@ -101,8 +101,8 @@ gsets_list <- get_gene_sets_list(
 ```
 
 ```{r, eval=TRUE}
-## see msigdbr::msigdbr_show_species() for all available organisms
-msigdbr::msigdbr_show_species()
+## see msigdbr::msigdbr_species() for all available organisms
+msigdbr::msigdbr_species()
 ```
 
 You may also obtain the gene sets for a subcollection by setting the `subcollection` argument: