inst/examples/optimization.R

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

\donttest{# example data from patRoonData package
dataDir <- patRoonData::exampleDataPath()
anaInfo <- generateAnalysisInfo(dataDir)
anaInfo <- anaInfo[1:2, ] # only focus on first two analyses (e.g. training set)

# optimize mzPPM and chromFWHM parameters
ftOpt <- optimizeFeatureFinding(anaInfo, "openms", list(mzPPM = c(5, 10), chromFWHM = c(4, 8)))

# optimize chromFWHM and isotopeFilteringModel (a qualitative parameter)
ftOpt2 <- optimizeFeatureFinding(anaInfo, "openms",
                                 list(isotopeFilteringModel = "metabolites (5% RMS)"),
                                 list(isotopeFilteringModel = "metabolites (2% RMS)"),
                                 templateParams = list(chromFWHM = c(4, 8)))

# perform grouping optimization with optimized features object
fgOpt <- optimizeFeatureGrouping(optimizedObject(ftOpt), "xcms",
                                 list(groupArgs = list(bw = c(22, 28)),
                                      retcorArgs = list(method = "obiwarp")))

# same, but using the XCMS3 interface
fgOpt2 <- optimizeFeatureGrouping(optimizedObject(ftOpt), "xcms3",
                                  list(groupMethod = "density", groupParams = list(bw = c(22, 28)),
                                       retAlignMethod = "obiwarp"))


# plot contour of first parameter set/DoE iteration
plot(ftOpt, paramSet = 1, DoEIteration = 1, type = "contour")

# generate parameter set with some predefined and custom parameters to be
# optimized.
pSet <- generateFeatureOptPSet("openms", chromSNR = c(3, 9),
                               useSmoothedInts = FALSE)
}