From dbd5781b6daf74ebae031cb9a91b0a61d95aa2d4 Mon Sep 17 00:00:00 2001
From: igor <6363505+igordot@users.noreply.github.com>
Date: Fri, 21 Feb 2025 10:10:15 -0500
Subject: [PATCH] Clean up documentation

---
 R/msigdbr.R    | 5 +++++
 R/zzz.R        | 2 +-
 man/msigdbr.Rd | 5 +++++
 3 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/R/msigdbr.R b/R/msigdbr.R
index bfe4ca0..e74188e 100644
--- a/R/msigdbr.R
+++ b/R/msigdbr.R
@@ -12,6 +12,11 @@
 #'
 #' Mouse MSigDB includes gene sets curated from mouse-centric datasets and specified in native mouse gene identifiers, eliminating the need for ortholog mapping.
 #'
+#' To access the full dataset, please install the msigdbdf package (not available on CRAN):
+#' ```
+#' install.packages("msigdbdf", repos = "https://igordot.r-universe.dev")
+#' ```
+#'
 #' @param species Species name for output genes, such as `"Homo sapiens"` or `"Mus musculus"`. Use `msigdbr_species()` for available options.
 #' @param db_species Species abbreviation for the human or mouse databases (`"HS"` or `"MM"`).
 #' @param collection Collection abbreviation, such as `"H"` or `"C1"`. Use `msigdbr_collections()` for the available options.
diff --git a/R/zzz.R b/R/zzz.R
index aa11bb7..70cc6af 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,7 +1,7 @@
 .onAttach <- function(libname, pkgname) {
   if (!requireNamespace("msigdbdf", quietly = TRUE)) {
     packageStartupMessage(
-      "To access all the data, please install the 'msigdbdf' package with:\n",
+      "For full functionality, please install the 'msigdbdf' package with:\n",
       "install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')"
     )
   }
diff --git a/man/msigdbr.Rd b/man/msigdbr.Rd
index 431d309..55ea033 100644
--- a/man/msigdbr.Rd
+++ b/man/msigdbr.Rd
@@ -42,6 +42,11 @@ The versioning convention of MSigDB is in the format \code{Year.Release.Species}
 The genes within each gene set may originate from a species different from the database target species as indicated by the \code{gs_source_species} and \code{db_target_species} fields.
 
 Mouse MSigDB includes gene sets curated from mouse-centric datasets and specified in native mouse gene identifiers, eliminating the need for ortholog mapping.
+
+To access the full dataset, please install the msigdbdf package (not available on CRAN):
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{install.packages("msigdbdf", repos = "https://igordot.r-universe.dev")
+}\if{html}{\out{</div>}}
 }
 \references{
 \url{https://www.gsea-msigdb.org/gsea/msigdb/index.jsp}