From 9d0887dfbf195828815d1994db06af111d4063b1 Mon Sep 17 00:00:00 2001
From: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: Thu, 3 Oct 2024 21:00:47 +0200
Subject: [PATCH] fix root directory

---
 vignettes/01-end-to-end-untargeted-metabolomics.qmd | 6 +++++-
 vignettes/alignment-to-external-dataset.qmd         | 6 +++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/vignettes/01-end-to-end-untargeted-metabolomics.qmd b/vignettes/01-end-to-end-untargeted-metabolomics.qmd
index b55ddea..a2d6d5a 100644
--- a/vignettes/01-end-to-end-untargeted-metabolomics.qmd
+++ b/vignettes/01-end-to-end-untargeted-metabolomics.qmd
@@ -12,6 +12,10 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
+```{r setup, include=FALSE}
+knitr::opts_knit$set(root.dir = './')
+```
+
 # Introduction
 
 The present workflow describes all steps for the analysis of an LC-MS/MS
@@ -1706,7 +1710,7 @@ Javascript as well as loaded easily back into R.
 # d <- file.path(tempdir(), "objects/lcms1")
 # saveMsObject(lcms1, AlabasterParam(path = d))
 #for now let's do R object because the previous method is not implemented yet. 
-save(lcms1, file = "objects/preprocessed_lcms1.RData")
+save(lcms1, file = "preprocessed_lcms1.RData")
 ```
 
 # Data normalization
diff --git a/vignettes/alignment-to-external-dataset.qmd b/vignettes/alignment-to-external-dataset.qmd
index 50ade20..c2b5286 100644
--- a/vignettes/alignment-to-external-dataset.qmd
+++ b/vignettes/alignment-to-external-dataset.qmd
@@ -10,6 +10,10 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
+```{r setup, include=FALSE}
+knitr::opts_knit$set(root.dir = './')
+```
+
 # Introduction
 
 In certain experiments, aligning datasets recorded at different times is
@@ -54,7 +58,7 @@ worflow](https://rformassspectrometry.github.io/metabonaut/articles/end-to-end-u
 vignette.
 
 ```{r}
-load("objects/preprocessed_lcms1.RData")
+load("preprocessed_lcms1.RData")
 ```
 
 ## Load unprocessed LC-MS/MS data