fix names

rformassspectrometry · Dec 9, 2024 · 2087ecb · 2087ecb
1 parent 9bf7913
commit 2087ecb
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/vignettes/a-end-to-end-untargeted-metabolomics.qmd b/vignettes/a-end-to-end-untargeted-metabolomics.qmd
@@ -41,7 +41,7 @@ alternatives](images/workflow.png)
 # Data description
 
 See the [data
-description](https://rformassspectrometry.github.io/metabonaut/articles/dataset-investigation.html)
+description](https://rformassspectrometry.github.io/Metabonaut/articles/dataset-investigation.html)
 vignette for detailed explanation of the dataset we go through in this workflow
 and general tips on what should be done when you first get your data.
 
@@ -256,7 +256,7 @@ As LC signal is the most variable because of the unstable nature of the LC, we
 will only show the BPC and their similarity. More in depth inspection and
 discussion of spectra and chromatrograhic data cna be found in the [data
 exploration
-vignette](https://rformassspectrometry.github.io/metabonaut/articles/data-investigation.html).
+vignette](https://rformassspectrometry.github.io/Metabonaut/articles/data-investigation.html).
 
 ## Chromatographic Data Visualization: BPC and TIC
 

diff --git a/vignettes/alignment-to-external-dataset.qmd b/vignettes/alignment-to-external-dataset.qmd
@@ -64,7 +64,7 @@ if (.Platform$OS.type == "unix") {
 First, let's load our pre-processed LC-MS object. This *xcms* result object was
 created during the [End-to-end
 worflow](https://rformassspectrometry.github.io/metabonaut/articles/end-to-end-untargeted-metabolomics.html)
-vignette and is also available in the *metabonaut* R package. The result object
+vignette and is also available in the *Metabonaut* R package. The result object
 (an `XcmsExperiment` object) was stored using Bioconductor's *alabaster*
 framework and we below load the object using the `readMsObject()` function
 providing the path to the stored data. The import function also takes care of
@@ -74,7 +74,7 @@ eventually retrieving missing MS data files from the MetaboLights repository.
 lcms1 <- readMsObject(
     XcmsExperiment(),
     AlabasterParam(system.file("extdata", "preprocessed_lcms1",
-                               package = "metabonaut")))
+                               package = "Metabonaut")))
 ```
 
 ## Load unprocessed LC-MS/MS data
@@ -154,7 +154,6 @@ bpc1 <-chromatogram(lcms1[c(idx_A,idx_E)], aggregationFun = "max",
 bpc2 <- chromatogram(lcms2, aggregationFun = "max", msLevel = 1)
 ```
 
-
 Compare run1 sample A with run2 sample A
 
 ```{r ini-bpc1}
@@ -195,6 +194,7 @@ mnpp <- MergeNeighboringPeaksParam(expandRt = 2.5, expandMz = 0.0015,
                                     minProp = 0.75)
 lcms2 <- refineChromPeaks(lcms2, param = mnpp, chunkSize = 2)
 ```
+
 ## Alignment
 
 Now, we will attempt to align these two samples with the previous dataset. The