Update Vignette

.github/workflows/check-bioc.yml

@@ -22,7 +22,8 @@
 
 on:
  push:
- pull_request:
+ paths-ignore:
+ - 'README.md'
 
 name: R-CMD-check-bioc
 

vignettes/MsBackendMetaboLights.Rmd

@@ -33,15 +33,15 @@ use of different *backends* to import MS data from a variety of sources and data
 formats. The *MsBackendMetaboLights* package allows to retrieve MS data files
 directly from the [MetaboLights](https://www.ebi.ac.uk/metabolights/)
 repository. MetaboLights is one of the main public repositories for deposition
-of metabolomics experiments including (raw) MS and/or NMR data files and
-experimental and analytical results. The *MsBackendMetaboLights* package
+of metabolomics experiments including (raw) MS and/or NMR data files and the
+related experimental and analytical results. The *MsBackendMetaboLights* package
 downloads and locally caches MS data files for a MetaboLights data set and
 enables further analyses of this data directly in R.
 
 
 # Installation
 
-To install this package, start `R` and enter:
+The package can be installed directly from within R with the few commands below:
 
 ```{r, eval = FALSE}
 if (!requireNamespace("BiocManager", quietly = TRUE))
@@ -50,7 +50,6 @@ if (!requireNamespace("BiocManager", quietly = TRUE))
 BiocManager::install("RforMassSpectrometry/MsBackendMetaboLights")
 ```
 
-This will install this package and all eventually missing dependencies.
 
 
 # Importing MS Data from MetaboLights
@@ -64,20 +63,22 @@ analyzed and at least one *assay* file that links between the experimental
 samples and the (raw and processed) data files with quantification of
 metabolites/features in these samples.
 
-In this vignette we explore and load a MS data files from a small MetaboLights
+In this vignette we explore and load MS data files from a small MetaboLights
 experiment. MetaboLights provides information on a data set/experiment as a set
-of plain text files in *ISA-tab* format. These consist generally of a file with
+of plain text files in *ISA-tab* format. These can be accessed and read from the
+data set's ftp folder. The set of files consist generally of a file with
 information on the experiment/investigation (in a file with the file name
 starting with *i_*) the samples of the data set (file name starting with *s_*),
 the *assay* (measurements/analysis) of the experiment and a file with quantified
 metabolite abundances (file name starting with *m_*). Note that a data set can
 have more than one assay file.
 
-Below we list all files from the MetaboLights data set with the ID MTBLS39.
+Below we list all files from the MetaboLights data set with the ID *MTBLS39*.
 
 ```{r}
 library(MsBackendMetaboLights)
 
+#' List files of a MetaboLights data set
 all_files <- mtbls_list_files("MTBLS39")
 ```
 
@@ -89,8 +90,10 @@ the ftp path for our test data set.
 mtbls_ftp_path("MTBLS39")
 ```
 
-The MS data files of a MetaboLights data set are defined in the assay data
-file(s) that we load below.
+We could inspect the content of this folder also using a browser supporting the
+ftp file transfer protocol and also download the files. We can however access
+the files also directly from within R. Below we read the *assay* data file
+directly using the `read.table()` function.
 
 ```{r}
 #' Get the assay files of the data set
@@ -123,15 +126,20 @@ Note that providing MS data files is not absolutely mandatory, thus, for some
 data sets no MS data files might be available. For this particular data set the
 MS data files are provided in the `"Raw Spectral Data File"` column. These files
 are in CDF format and can hence be loaded using the `MsBackendMetaboLights`
-backend into R as a `Spectra` object. By default, all MS data files of all
+backend into R as a `Spectra` object (`MsBackendMetaboLights` directly extends
+*Spectra*'s `MsBackendMzR` backend and therefore supports import of MS data
+files in mzML, CDF or mzXML formats). By default, all MS data files of all
 assays would be retrieved, but in our example below we restrict to few files to
 reduce the amount of data that needs to be downloaded. We define for that a
 pattern matching the file name of only some data files using the `filePattern`
-parameter. In our case we load all MS data files that end with *63A.cdf*.
+parameter. Alternatively, for data sets with more than one assay, it would also
+be possible to select MS data files from one particular assay only using the
+`assayId` parameter. In our case we load all MS data files that end with *63A.cdf*.
 
 ```{r}
 library(Spectra)
 
+#' Load MS data files of one data set
 s <- Spectra("MTBLS39", filePattern = "63A.cdf",
  source = MsBackendMetaboLights())
 s
@@ -166,6 +174,9 @@ spectraData(s, c("mtbls_id", "mtbls_assay_name",
  "derived_spectral_data_file"))
 ```
 
+These variables can also be used to e.g. link the individual spectra back to the
+original sample (e.g. through the *assay* and *sample* tables of the
+MetaboLights data set.
 
 
 # Session information