Description Usage Arguments Details Value Slots Note Author(s) See Also Examples
This method performs a two-step centWave-based chromatographic peak detection: in a first centWave run peaks are identified for which then the location of their potential isotopes in the mz-retention time is predicted. A second centWave run is then performed on these regions of interest (ROIs). The final list of chromatographic peaks comprises all non-overlapping peaks from both centWave runs.
The CentWavePredIsoParam
class allows to specify all
settings for the two-step centWave-based peak detection considering also
predicted isotopes of peaks identified in the first centWave run.
Instances should be created with the CentWavePredIsoParam
constructor. See also the documentation of the
CentWaveParam
for all methods and arguments this class
inherits.
The findChromPeaks,OnDiskMSnExp,CentWavePredIsoParam
method performs a two-step centWave-based chromatographic peak detection
on all samples from an OnDiskMSnExp
object.
OnDiskMSnExp
objects encapsule all experiment
specific data and load the spectra data (mz and intensity values) on the
fly from the original files applying also all eventual data
manipulations.
snthreshIsoROIs
,snthreshIsoROIs<-
: getter and
setter for the snthreshIsoROIs
slot of the object.
maxCharge
,maxCharge<-
: getter and
setter for the maxCharge
slot of the object.
maxIso
,maxIso<-
: getter and
setter for the maxIso
slot of the object.
mzIntervalExtension
,mzIntervalExtension<-
: getter
and setter for the mzIntervalExtension
slot of the object.
polarity
,polarity<-
: getter and
setter for the polarity
slot of the object.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 | CentWavePredIsoParam(
ppm = 25,
peakwidth = c(20, 50),
snthresh = 10,
prefilter = c(3, 100),
mzCenterFun = "wMean",
integrate = 1L,
mzdiff = -0.001,
fitgauss = FALSE,
noise = 0,
verboseColumns = FALSE,
roiList = list(),
firstBaselineCheck = TRUE,
roiScales = numeric(),
snthreshIsoROIs = 6.25,
maxCharge = 3,
maxIso = 5,
mzIntervalExtension = TRUE,
polarity = "unknown"
)
## S4 method for signature 'OnDiskMSnExp,CentWavePredIsoParam'
findChromPeaks(
object,
param,
BPPARAM = bpparam(),
return.type = "XCMSnExp",
msLevel = 1L
)
## S4 method for signature 'CentWavePredIsoParam'
show(object)
## S4 method for signature 'CentWavePredIsoParam'
snthreshIsoROIs(object)
## S4 replacement method for signature 'CentWavePredIsoParam'
snthreshIsoROIs(object) <- value
## S4 method for signature 'CentWavePredIsoParam'
maxCharge(object)
## S4 replacement method for signature 'CentWavePredIsoParam'
maxCharge(object) <- value
## S4 method for signature 'CentWavePredIsoParam'
maxIso(object)
## S4 replacement method for signature 'CentWavePredIsoParam'
maxIso(object) <- value
## S4 method for signature 'CentWavePredIsoParam'
mzIntervalExtension(object)
## S4 replacement method for signature 'CentWavePredIsoParam'
mzIntervalExtension(object) <- value
## S4 method for signature 'CentWavePredIsoParam'
polarity(object)
## S4 replacement method for signature 'CentWavePredIsoParam'
polarity(object) <- value
|
ppm |
|
peakwidth |
|
snthresh |
|
prefilter |
|
mzCenterFun |
Name of the function to calculate the m/z center of the
chromatographic peak. Allowed are: |
integrate |
Integration method. For |
mzdiff |
|
fitgauss |
|
noise |
|
verboseColumns |
|
roiList |
An optional list of regions-of-interest (ROI) representing
detected mass traces. If ROIs are submitted the first analysis step is
omitted and chromatographic peak detection is performed on the submitted
ROIs. Each ROI is expected to have the following elements specified:
|
firstBaselineCheck |
|
roiScales |
Optional numeric vector with length equal to |
snthreshIsoROIs |
|
maxCharge |
|
maxIso |
|
mzIntervalExtension |
|
polarity |
|
object |
For For all other methods: a parameter object. |
param |
An |
BPPARAM |
A parameter class specifying if and how parallel processing
should be performed. It defaults to |
return.type |
Character specifying what type of object the method should
return. Can be either |
msLevel |
|
value |
The value for the slot. |
See centWave
for details on the centWave method.
Parallel processing (one process per sample) is supported and can
be configured either by the BPPARAM
parameter or by globally
defining the parallel processing mode using the
register
method from the BiocParallel
package.
The CentWavePredIsoParam
function returns a
CentWavePredIsoParam
class instance with all of the settings
specified for the two-step centWave-based peak detection considering also
isotopes.
For findChromPeaks
: if return.type = "XCMSnExp"
an
XCMSnExp
object with the results of the peak detection.
If return.type = "list"
a list of length equal to the number of
samples with matrices specifying the identified peaks.
If return.type = "xcmsSet"
an xcmsSet
object
with the results of the peak detection.
.__classVersion__,ppm,peakwidth,snthresh,prefilter,mzCenterFun,integrate,mzdiff,fitgauss,noise,verboseColumns,roiList,firstBaselineCheck,roiScales,snthreshIsoROIs,maxCharge,maxIso,mzIntervalExtension,polarity
See corresponding parameter above. .__classVersion__
stores
the version from the class. Slots values should exclusively be accessed
via the corresponding getter and setter methods listed above.
These methods and classes are part of the updated and modernized
xcms
user interface which will eventually replace the
findPeaks
methods. It supports chromatographic peak
detection on
OnDiskMSnExp
objects (defined in the
MSnbase
package). All of the settings to the algorithm can be
passed with a CentWavePredIsoParam
object.
Hendrik Treutler, Johannes Rainer
The do_findChromPeaks_centWaveWithPredIsoROIs
core
API function and findPeaks.centWave
for the old user
interface. CentWaveParam
for the class the
CentWavePredIsoParam
extends.
XCMSnExp
for the object containing the results of
the peak detection.
Other peak detection methods:
chromatographic-peak-detection
,
findChromPeaks-centWave
,
findChromPeaks-massifquant
,
findChromPeaks-matchedFilter
,
findPeaks-MSW
1 2 3 4 5 | ## Create a param object
p <- CentWavePredIsoParam(maxCharge = 4)
## Change snthresh parameter
snthresh(p) <- 25
p
|
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