From 7c9e7d390e181445d48a05f2c3aa80d9f94e978b Mon Sep 17 00:00:00 2001
From: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: Wed, 30 Oct 2024 15:32:54 +0100
Subject: [PATCH] fix: .rt_model only use 2 columns instead of all

---
 R/do_adjustRtime-functions.R |  2 +-
 vignettes/xcms.Rmd           | 12 ++++--------
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/R/do_adjustRtime-functions.R b/R/do_adjustRtime-functions.R
index 1fe5282c..b432daf2 100644
--- a/R/do_adjustRtime-functions.R
+++ b/R/do_adjustRtime-functions.R
@@ -874,7 +874,7 @@ NULL
                       resid_ratio = 3,
                       zero_weight = 10,
                       bs = "tp"){
-    rt_map <- rt_map[order(rt_map$obs), ]
+    rt_map <- rt_map[order(rt_map$obs), c("ref", "obs")]
     # add first row of c(0,0) to set a fix timepoint.
     rt_map <- rbind(c(0,0), rt_map)
     weights <- rep(1, nrow(rt_map))
diff --git a/vignettes/xcms.Rmd b/vignettes/xcms.Rmd
index 0382314b..02abbe13 100644
--- a/vignettes/xcms.Rmd
+++ b/vignettes/xcms.Rmd
@@ -1203,17 +1203,13 @@ f[f != "QC"] <- NA
 f <- sampleData(faahko)$sample_type
 f[f == "QC"] <- NA
 
-missing_filter <- PercentMissingFilter(threshold = 30,
-                                       f = f)
+missing_filter <- PercentMissingFilter(threshold = 30, f = f)
 # Apply the filter to faakho object
-filtered_faahko <- filterFeatures(object = faahko,
-                                  filter = missing_filter)
+filtered_faahko <- filterFeatures(object = faahko, filter = missing_filter)
 
 # Apply the filter to res object
-missing_filter <- PercentMissingFilter(threshold = 30,
-                                       f = f)
-filtered_res <- filterFeatures(object = res,
-                               filter = missing_filter)
+missing_filter <- PercentMissingFilter(threshold = 30, f = f)
+filtered_res <- filterFeatures(object = res, filter = missing_filter)
 ```
 
 Here, no feature was removed, meaning that all the features had less than 30%