diff --git a/vignettes/RMassBankXCMS.Rnw b/vignettes/RMassBankXCMS.Rnw index 0d2663e0c56fa52337d50505d3dc6d2379d41d16..fab7c72d6876a7e645fc287a203dfb9af234de34 100644 --- a/vignettes/RMassBankXCMS.Rnw +++ b/vignettes/RMassBankXCMS.Rnw @@ -124,13 +124,18 @@ Please note that "findPeaksArgs" has to be a list with the list elements named a For example, if you want to use centWave with a peakwidth from 5 to 10 and 25 ppm, findPeaksArgs would look like this: <<eval=TRUE>>= - Args <- list(method="centWave", peakwidth=c(5,12), prefilter=c(0,0), ppm=25, snthr=2) + Args <- list(method="centWave", + peakwidth=c(5,12), + prefilter=c(0,0), + ppm=25, snthr=2) @ If you want to utilize XCMS for Step 1 of the workflow, you have to set the readMethod-parameter to "xcms" and - if you don't want to use standard values for findPeaks - pass on findPeaksArgs to the workflow. <<eval=TRUE>>= - msmsList <- msmsWorkflow(msmsList, steps=1:8, mode="mH", readMethod="xcms", findPeaksArgs = Args) + msmsList <- msmsWorkflow(msmsList, steps=1:8, + mode="mH", readMethod="xcms", + findPeaksArgs = Args) @ You can of course run the rest of the workflow as usual, by - like here - setting steps to 1:8 @@ -143,8 +148,11 @@ The readMethod name for this is "peaklist" <<eval=FALSE>>= msmsPeaklist <- newMsmsWorkspace() - msmsPeaklist@files <- list.files(system.file("spectra.Glucolesquerellin", package = "RMassBankData"), "Glucolesquerellin.*csv", full.names=TRUE) - msmsPeaklist <- msmsWorkflow(msmsPeaklist, steps=1:8, mode="mH", readMethod="peaklist") + msmsPeaklist@files <- list.files(system.file("spectra.Glucolesquerellin", + package = "RMassBankData"), + "Glucolesquerellin.*csv", full.names=TRUE) + msmsPeaklist <- msmsWorkflow(msmsPeaklist, steps=1:8, + mode="mH", readMethod="peaklist") @ \subsection{Export the records} @@ -155,7 +163,8 @@ This section is just to debug the record creation with XCMS, and hence very ters <<>>= mb <- newMbWorkspace(msmsList) mb <- resetInfolists(mb) -mb <- loadInfolist(mb,system.file("infolists/PlantDataset.csv", package = "RMassBankData")) +mb <- loadInfolist(mb,system.file("infolists/PlantDataset.csv", + package = "RMassBankData")) ## Step mb <- mbWorkflow(mb, steps=3:4) @