Description Usage Arguments Details Value Slots Note Author(s) References See Also Examples
The matchedFilter algorithm identifies peaks in the
chromatographic time domain as described in [Smith 2006]. The intensity
values are binned by cutting The LC/MS data into slices (bins) of a mass
unit (binSize
m/z) wide. Within each bin the maximal intensity is
selected. The chromatographic peak detection is then performed in each
bin by extending it based on the steps
parameter to generate
slices comprising bins current_bin - steps +1
to
current_bin + steps - 1
. Each of these slices is then filtered
with matched filtration using a second-derative Gaussian as the model
peak shape. After filtration peaks are detected using a signal-to-ratio
cut-off. For more details and illustrations see [Smith 2006].
The MatchedFilterParam
class allows to specify all
settings for a chromatographic peak detection using the matchedFilter
method. Instances should be created with the MatchedFilterParam
constructor.
The findChromPeaks,OnDiskMSnExp,MatchedFilterParam
method performs peak detection using the matchedFilter 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.
binSize
,binSize<-
: getter and setter for the
binSize
slot of the object.
impute
,impute<-
: getter and setter for the
impute
slot of the object.
baseValue
,baseValue<-
: getter and setter for the
baseValue
slot of the object.
distance
,distance<-
: getter and setter for the
distance
slot of the object.
fwhm
,fwhm<-
: getter and setter for the
fwhm
slot of the object.
sigma
,sigma<-
: getter and setter for the
sigma
slot of the object.
max
,max<-
: getter and setter for the
max
slot of the object.
snthresh
,snthresh<-
: getter and setter for the
snthresh
slot of the object.
steps
,steps<-
: getter and setter for the
steps
slot of the object.
mzdiff
,mzdiff<-
: getter and setter for the
mzdiff
slot of the object.
index
,index<-
: getter and setter for the
index
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 | MatchedFilterParam(
binSize = 0.1,
impute = "none",
baseValue = numeric(),
distance = numeric(),
fwhm = 30,
sigma = fwhm/2.3548,
max = 5,
snthresh = 10,
steps = 2,
mzdiff = 0.8 - binSize * steps,
index = FALSE
)
## S4 method for signature 'OnDiskMSnExp,MatchedFilterParam'
findChromPeaks(
object,
param,
BPPARAM = bpparam(),
return.type = "XCMSnExp",
msLevel = 1L
)
## S4 method for signature 'MatchedFilterParam'
show(object)
## S4 method for signature 'MatchedFilterParam'
binSize(object)
## S4 replacement method for signature 'MatchedFilterParam'
binSize(object) <- value
## S4 method for signature 'MatchedFilterParam'
impute(object)
## S4 replacement method for signature 'MatchedFilterParam'
impute(object) <- value
## S4 method for signature 'MatchedFilterParam'
baseValue(object)
## S4 replacement method for signature 'MatchedFilterParam'
baseValue(object) <- value
## S4 method for signature 'MatchedFilterParam'
distance(object)
## S4 replacement method for signature 'MatchedFilterParam'
distance(object) <- value
## S4 method for signature 'MatchedFilterParam'
fwhm(object)
## S4 replacement method for signature 'MatchedFilterParam'
fwhm(object) <- value
## S4 method for signature 'MatchedFilterParam'
sigma(object)
## S4 replacement method for signature 'MatchedFilterParam'
sigma(object) <- value
## S4 method for signature 'MatchedFilterParam'
max(x)
## S4 replacement method for signature 'MatchedFilterParam'
max(object) <- value
## S4 method for signature 'MatchedFilterParam'
snthresh(object)
## S4 replacement method for signature 'MatchedFilterParam'
snthresh(object) <- value
## S4 method for signature 'MatchedFilterParam'
steps(object)
## S4 replacement method for signature 'MatchedFilterParam'
steps(object) <- value
## S4 method for signature 'MatchedFilterParam'
mzdiff(object)
## S4 replacement method for signature 'MatchedFilterParam'
mzdiff(object) <- value
## S4 method for signature 'MatchedFilterParam'
index(object)
## S4 replacement method for signature 'MatchedFilterParam'
index(object) <- value
|
binSize |
|
impute |
Character string specifying the method to be used for missing
value imputation. Allowed values are |
baseValue |
The base value to which empty elements should be set. This
is only considered for |
distance |
For |
fwhm |
|
sigma |
|
max |
|
snthresh |
|
steps |
|
mzdiff |
|
index |
|
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. |
x |
For |
The intensities are binned by the provided m/z values within each
spectrum (scan). Binning is performed such that the bins are centered
around the m/z values (i.e. the first bin includes all m/z values between
min(mz) - bin_size/2
and min(mz) + bin_size/2
).
For more details on binning and missing value imputation see
binYonX
and imputeLinInterpol
methods.
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 MatchedFilterParam
function returns a
MatchedFilterParam
class instance with all of the settings
specified for chromatographic detection by the matchedFilter
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__,binSize,impute,baseValue,distance,fwhm,sigma,max,snthresh,steps,mzdiff,index
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 matchedFilter
algorithm can be passed with a MatchedFilterParam
object.
Colin A Smith, Johannes Rainer
Colin A. Smith, Elizabeth J. Want, Grace O'Maille, Ruben Abagyan and Gary Siuzdak. "XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification" Anal. Chem. 2006, 78:779-787.
The do_findChromPeaks_matchedFilter
core API function
and findPeaks.matchedFilter
for the old user interface.
peaksWithMatchedFilter
for functions to perform matchedFilter
peak detection in purely chromatographic data.
XCMSnExp
for the object containing the results of
the chromatographic peak detection.
Other peak detection methods:
chromatographic-peak-detection
,
findChromPeaks-centWaveWithPredIsoROIs
,
findChromPeaks-centWave
,
findChromPeaks-massifquant
,
findPeaks-MSW
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## Create a MatchedFilterParam object. Note that we use a unnecessarily large
## binSize parameter to reduce the run-time of the example.
mfp <- MatchedFilterParam(binSize = 5)
## Change snthresh parameter
snthresh(mfp) <- 15
mfp
## Perform the peak detection using matchecFilter 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 chromatographic peak detection using the settings defined
## above. Note that we are also disabling parallel processing in this
## example by registering a "SerialParam"
res <- findChromPeaks(raw_data, param = mfp)
head(chromPeaks(res))
|
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