Update RMassBankXCMS.Rnw

Fixed minor errors, reordered 3.3 and 3.4 to avoid confusion, mentioned msmsRead.

vignettes/RMassBankXCMS.Rnw

@@ -39,7 +39,7 @@ options(width=74)
 \section{Introduction}
 
 As the RMassBank-workflow is described in the other manual, this document mainly explains how to utilize the
-XCMS-, MassBank-, andpeaklist-readMethods for step 1 of the workflow.
+XCMS-, MassBank-, and peaklist-readMethods for Step 1 of the workflow.
 
 \section{Input files}
 
@@ -50,14 +50,14 @@ centroid\footnote{The term "centroid" here refers to any kind of data which are
 not in profile mode, i.e. don't have continuous m/z data. It does not refer to
 the (mathematical) centroid peak, i.e. the area-weighted mass peak.} or in
 profile mode.
-Data in the examples was acquired using an QTOF instrument.
+Data in the examples was acquired using a QTOF instrument.
 
 In the standard workflow, the file names are used to identify a
 compound: file names must be in the format \funcarg{xxxxxxxx\_1234\_xxx.mzXML},
 where the xxx parts denote anything and the 1234 part denotes the compound ID in
 the compound list (see below). Advanced and alternative uses can be implemented;
-consult the implementation of \Rvar{msms\_workflow} and \Rvar{findMsMsHRperX.direct} for
-more information.
+consult the implementation of \Rvar{msmsRead}, \Rvar{msms\_workflow} and 
+\Rvar{findMsMsHRperX.direct} for more information.
 
 \section{Additional Workflow-Methods}
 
@@ -73,7 +73,7 @@ library(RMassBankData)
 
 In the first part of the workflow, spectra are extracted from the
 files and processed. In the following example, we will process the
-Glulesquerellin spectra from the provided files.
+Glucolesquerellin spectra from the provided files.
 
 For the workflow to work correctly, we use the default settings, and
 modify then to match the data acquisition method. The settings have to
@@ -159,6 +159,21 @@ msmsList <- msmsWorkflow(msmsList, steps=2:8,
 
 You can of course run the rest of the workflow as usual, by - like here - setting steps to 1:8
 
+\subsection{Export the records}
+
+To export the records from the XCMS workflow, follow the same procedure 
+as the standard RMassBank workflow, i.e.:
+
+
+<<>>=
+mb <- newMbWorkspace(msmsList)
+mb <- resetInfolists(mb)
+mb <- loadInfolist(mb,system.file("infolists/PlantDataset.csv",
+                                  package = "RMassBankData"))
+## Step
+mb <- mbWorkflow(mb, steps=1:8)
+@
+
 \subsection{peaklist-workflow}
 
 The peaklist-workflow works akin to the normal mzR-workflow with the
@@ -178,21 +193,7 @@ msmsPeaklist <- msmsWorkflow(msmsPeaklist, steps=1:8,
                              mode="mH", readMethod="peaklist")
 @
 
-\subsection{Export the records}
-
-This section is just to debug the record creation with XCMS, and hence very terse.
-
-
-<<>>=
-mb <- newMbWorkspace(msmsList)
-mb <- resetInfolists(mb)
-mb <- loadInfolist(mb,system.file("infolists/PlantDataset.csv",
-                                  package = "RMassBankData"))
-## Step
-mb <- mbWorkflow(mb, steps=1:8)
-@
-
-
+The records can then be generated and exported with \Rfunction{mbWorkflow}.
 
 
 \section{Session information}