Check suggested packages for function tests

Author: mass-a

DESCRIPTION

@@ -29,7 +29,6 @@ Imports: RcppML,
 Suggests: knitr,
     rmarkdown,
     fgsea,
-    dplyr,
     msigdbr
 VignetteBuilder: knitr
 URL: https://github.com/carmonalab/GeneNMF

R/main.R

@@ -429,8 +429,9 @@ plotMetaPrograms <- function(mp.res,
 
 #' Run Gene set enrichment analysis
 #'
-#' Utility function to run Gene set enrichment analysis (GSEA) against gene 
-#' sets from MSigDB.
+#' Utility function to run Gene Set Enrichment Analysis (GSEA) against gene 
+#' sets from MSigDB. Note: this is an optional function, which is conditional
+#' to the installation of suggested packages \code{fgsea} and \code{msigdbr}.
 #'
 #' @param genes A vector of genes
 #' @param universe Background universe of gene symbols (passed on to \code{fgsea::fora})
@@ -444,7 +445,13 @@ plotMetaPrograms <- function(mp.res,
 #' @examples
 #' data(sampleObj)
 #' geneset <- c("BANK1","CD22","CD79A","CD19","IGHD","IGHG3","IGHM")
-#' gsea_res <- runGSEA(geneset, universe=rownames(sampleObj), category = "C8")
+#' #test is conditional on availability of suggested packages
+#' if (requireNamespace("fgsea", quietly=TRUE) &
+#'    requireNamespace("msigdbr", quietly=TRUE)) {
+#'    gsea_res <- runGSEA(geneset,
+#'        universe=rownames(sampleObj),
+#'        category = "C8")
+#' }
 #' 
 #' @export  
 runGSEA <- function(genes, universe=NULL,