Description Usage Arguments Details Value Slots Note Author(s) References See Also Examples
Massifquant is a Kalman filter (KF)-based chromatographic peak
detection for XC-MS data in centroid mode. The identified peaks
can be further refined with the centWave method (see
findChromPeaks-centWave
for details on centWave)
by specifying withWave = TRUE
.
The MassifquantParam
class allows to specify all
settings for a chromatographic peak detection using the massifquant
method eventually in combination with the centWave algorithm. Instances
should be created with the MassifquantParam
constructor.
The findChromPeaks,OnDiskMSnExp,MassifquantParam
method performs chromatographic peak detection using the
massifquant algorithm 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.
ppm
,ppm<-
: getter and setter for the ppm
slot of the object.
peakwidth
,peakwidth<-
: getter and setter for the
peakwidth
slot of the object.
snthresh
,snthresh<-
: getter and setter for the
snthresh
slot of the object.
prefilter
,prefilter<-
: getter and setter for the
prefilter
slot of the object.
mzCenterFun
,mzCenterFun<-
: getter and setter for the
mzCenterFun
slot of the object.
integrate
,integrate<-
: getter and setter for the
integrate
slot of the object.
mzdiff
,mzdiff<-
: getter and setter for the
mzdiff
slot of the object.
fitgauss
,fitgauss<-
: getter and setter for the
fitgauss
slot of the object.
noise
,noise<-
: getter and setter for the
noise
slot of the object.
verboseColumns
,verboseColumns<-
: getter and
setter for the verboseColumns
slot of the object.
criticalValue
,criticalValue<-
: getter and
setter for the criticalValue
slot of the object.
consecMissedLimit
,consecMissedLimit<-
: getter and
setter for the consecMissedLimit
slot of the object.
unions
,unions<-
: getter and
setter for the unions
slot of the object.
checkBack
,checkBack<-
: getter and
setter for the checkBack
slot of the object.
withWave
,withWave<-
: getter and
setter for the withWave
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 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 | MassifquantParam(
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,
criticalValue = 1.125,
consecMissedLimit = 2,
unions = 1,
checkBack = 0,
withWave = FALSE
)
## S4 method for signature 'OnDiskMSnExp,MassifquantParam'
findChromPeaks(
object,
param,
BPPARAM = bpparam(),
return.type = "XCMSnExp",
msLevel = 1L
)
## S4 method for signature 'MassifquantParam'
show(object)
## S4 method for signature 'MassifquantParam'
ppm(object)
## S4 replacement method for signature 'MassifquantParam'
ppm(object) <- value
## S4 method for signature 'MassifquantParam'
peakwidth(object)
## S4 replacement method for signature 'MassifquantParam'
peakwidth(object) <- value
## S4 method for signature 'MassifquantParam'
snthresh(object)
## S4 replacement method for signature 'MassifquantParam'
snthresh(object) <- value
## S4 method for signature 'MassifquantParam'
prefilter(object)
## S4 replacement method for signature 'MassifquantParam'
prefilter(object) <- value
## S4 method for signature 'MassifquantParam'
mzCenterFun(object)
## S4 replacement method for signature 'MassifquantParam'
mzCenterFun(object) <- value
## S4 method for signature 'MassifquantParam'
integrate(f)
## S4 replacement method for signature 'MassifquantParam'
integrate(object) <- value
## S4 method for signature 'MassifquantParam'
mzdiff(object)
## S4 replacement method for signature 'MassifquantParam'
mzdiff(object) <- value
## S4 method for signature 'MassifquantParam'
fitgauss(object)
## S4 replacement method for signature 'MassifquantParam'
fitgauss(object) <- value
## S4 method for signature 'MassifquantParam'
noise(object)
## S4 replacement method for signature 'MassifquantParam'
noise(object) <- value
## S4 method for signature 'MassifquantParam'
verboseColumns(object)
## S4 replacement method for signature 'MassifquantParam'
verboseColumns(object) <- value
## S4 method for signature 'MassifquantParam'
criticalValue(object)
## S4 replacement method for signature 'MassifquantParam'
criticalValue(object) <- value
## S4 method for signature 'MassifquantParam'
consecMissedLimit(object)
## S4 replacement method for signature 'MassifquantParam'
consecMissedLimit(object) <- value
## S4 method for signature 'MassifquantParam'
unions(object)
## S4 replacement method for signature 'MassifquantParam'
unions(object) <- value
## S4 method for signature 'MassifquantParam'
checkBack(object)
## S4 replacement method for signature 'MassifquantParam'
checkBack(object) <- value
## S4 method for signature 'MassifquantParam'
withWave(object)
## S4 replacement method for signature 'MassifquantParam'
withWave(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 |
|
criticalValue |
|
consecMissedLimit |
|
unions |
|
checkBack |
|
withWave |
|
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. |
f |
For |
This algorithm's performance has been tested rigorously
on high resolution LC/OrbiTrap, TOF-MS data in centroid mode.
Simultaneous kalman filters identify chromatographic peaks and calculate
their area under the curve. The default parameters are set to operate on
a complex LC-MS Orbitrap sample. Users will find it useful to do some
simple exploratory data analysis to find out where to set a minimum
intensity, and identify how many scans an average peak spans. The
consecMissedLimit
parameter has yielded good performance on
Orbitrap data when set to (2
) and on TOF data it was found best
to be at (1
). This may change as the algorithm has yet to be
tested on many samples. The criticalValue
parameter is perhaps
most dificult to dial in appropriately and visual inspection of peak
identification is the best suggested tool for quick optimization.
The ppm
and checkBack
parameters have shown less influence
than the other parameters and exist to give users flexibility and
better accuracy.
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 MassifquantParam
function returns a
MassifquantParam
class instance with all of the settings
specified for chromatographic peak detection by the massifquant
method.
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,criticalValue,consecMissedLimit,unions,checkBack,withWave
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 massifquant and
centWave algorithm can be passed with a MassifquantParam
object.
Christopher Conley, Johannes Rainer
Conley CJ, Smith R, Torgrip RJ, Taylor RM, Tautenhahn R and Prince JT "Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection" Bioinformatics 2014, 30(18):2636-43.
The do_findChromPeaks_massifquant
core API function
and findPeaks.massifquant
for the old user interface.
XCMSnExp
for the object containing the results of
the peak detection.
Other peak detection methods:
chromatographic-peak-detection
,
findChromPeaks-centWaveWithPredIsoROIs
,
findChromPeaks-centWave
,
findChromPeaks-matchedFilter
,
findPeaks-MSW
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## Create a MassifquantParam object.
mqp <- MassifquantParam()
## Change snthresh prefilter parameters
snthresh(mqp) <- 30
prefilter(mqp) <- c(6, 10000)
mqp
## Perform the peak detection using massifquant on the files from the
## faahKO package. Files are read using the readMSData from the MSnbase
## package
library(faahKO)
library(MSnbase)
fls <- dir(system.file("cdf/KO", package = "faahKO"), recursive = TRUE,
full.names = TRUE)
raw_data <- readMSData(fls[1], mode = "onDisk")
## Perform the peak detection using the settings defined above.
res <- findChromPeaks(raw_data, param = mqp)
head(chromPeaks(res))
|
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