From dd81914834144f23ad56196e45833d837754e35b Mon Sep 17 00:00:00 2001
From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com>
Date: Thu, 9 Nov 2023 09:50:47 +0000
Subject: [PATCH] Fix vignette

---
 R/merge_results.R       | 2 +-
 vignettes/MultiEWCE.Rmd | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/merge_results.R b/R/merge_results.R
index 5041c82..563ebb8 100644
--- a/R/merge_results.R
+++ b/R/merge_results.R
@@ -30,7 +30,7 @@ merge_results <- function(save_dir=NULL,
   if(is.null(res_files)){
     if(is.null(save_dir)) stop("Must provided save_dir when res_files=NULL.")
     res_files <- list.files(path = save_dir,
-                            pattern = ".rds$",
+                            pattern = "\\.rds$",
                             ignore.case = TRUE,
                             full.names = TRUE)
     names(res_files) <- gsub("_"," ",tolower(gsub(".rds$","",res_files)))
diff --git a/vignettes/MultiEWCE.Rmd b/vignettes/MultiEWCE.Rmd
index 5efd719..f334ffb 100644
--- a/vignettes/MultiEWCE.Rmd
+++ b/vignettes/MultiEWCE.Rmd
@@ -52,7 +52,7 @@ ctd <- load_example_ctd()
 list_names <- unique(gene_data$hpo_id)[seq(10)] 
 reps <- 10 # in practice would use more reps
 cores <- 1 # in practice would use more cores
-save_dir <- tempdir()
+save_dir <- file.path(tempdir())
 save_dir_tmp <- file.path(save_dir,"results")
 ```
 
@@ -131,7 +131,7 @@ methods::show(plot1)
 ## merge_results 
 If you have a results directory of individual EWCE results but do not have the merged dataframe of all results, you can call the `merge_results` function manually. The `save_dir` argument is the path to your results directory and the `list_name_column` argument is the name of the column containing gene list names. In this case we used "Phenotype" as this column name when we generated the results.
 
-```{r merge}
+```{r merge, eval=FALSE}
 all_results_2 <- MultiEWCE::merge_results(save_dir = save_dir_tmp)
 ```