dontrun bugsigdb examples

noriakis · Apr 18, 2024 · a3b9852 · a3b9852
1 parent 944e160
commit a3b9852
Show file tree

Hide file tree

Showing 4 changed files with 18 additions and 2 deletions.
diff --git a/R/external.R b/R/external.R
@@ -8,6 +8,11 @@
 #' @param keyType key type of gene
 #' @param argList argument list to pass to refseq()
 #' @export
+#' @examples
+#' cols <- sample(c(1), 6, replace=TRUE)
+#' names(cols) <- c("PNKP","ERCC2","ERCC3","IRF3","TP53","MCM6")
+#' wg <- list("colors"=cols)
+#' refseqWGCNA(wg, keyType="SYMBOL")
 #' @return list of biotext class object
 refseqWGCNA <- function(wgcna, keyType="ENSEMBL", argList=list()) {
     all_cols <- unique(wgcna$colors)

diff --git a/R/steps.R b/R/steps.R
@@ -71,7 +71,10 @@ obtain_alliance <- function(geneList, file="GENE-DESCRIPTION-TSV_HUMAN.tsv",
 #' @param curate curated articles (TRUE) or search for PubMed (FALSE)
 #' if FALSE, same for fetching from PubMed by specified query
 #' @export
-#' @examples obtain_bugsigdb("Veillonella dispar")
+#' @examples 
+#' \dontrun{
+#'     obtain_bugsigdb("Veillonella dispar")
+#' }
 #' @return biotext class object
 obtain_bugsigdb <- function(mb_list,
 	target="title",

diff --git a/man/obtain_bugsigdb.Rd b/man/obtain_bugsigdb.Rd
diff --git a/man/refseqWGCNA.Rd b/man/refseqWGCNA.Rd