Description Usage Arguments Value Slots Note References See Also Examples
This method is inspired by the grouping algorithm of mzMine (Katajamaa 2006) and performs correspondence based on proximity of peaks in the space spanned by retention time and mz values. The method creates first a master peak list consisting of all chromatographic peaks from the sample in which most peaks were identified, and starting from that, calculates distances to peaks from the sample with the next most number of peaks. If peaks are closer than the defined threshold they are grouped together.
The NearestPeaksParam
class allows to specify all
settings for the peak grouping based on the nearest algorithm.
Instances should be created with the NearestPeaksParam
constructor.
sampleGroups
,sampleGroups<-
: getter and setter
for the sampleGroups
slot of the object.
mzVsRtBalance
,mzVsRtBalance<-
: getter and setter
for the mzVsRtBalance
slot of the object.
absMz
,absMz<-
: getter and setter for the
absMz
slot of the object.
absRt
,absRt<-
: getter and setter for the
absRt
slot of the object.
kNN
,kNN<-
: getter and setter for the
kNN
slot of the object.
groupChromPeaks,XCMSnExp,NearestPeaksParam
:
performs peak grouping based on the proximity between chromatographic
peaks from different samples in the mz-rt range.
The correspondence analysis can be performed on chromatographic peaks of
any MS level (if present and if chromatographic peak detection has been
performed for that MS level) defining features combining these peaks. The
MS level can be selected with the parameter msLevel
. By default, calling
groupChromPeaks
will remove any previous correspondence results. This can
be disabled with add = TRUE
, which will add newly defined features to
already present feature definitions.
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 | NearestPeaksParam(
sampleGroups = numeric(),
mzVsRtBalance = 10,
absMz = 0.2,
absRt = 15,
kNN = 10
)
## S4 method for signature 'NearestPeaksParam'
show(object)
## S4 method for signature 'NearestPeaksParam'
sampleGroups(object)
## S4 replacement method for signature 'NearestPeaksParam'
sampleGroups(object) <- value
## S4 method for signature 'NearestPeaksParam'
mzVsRtBalance(object)
## S4 replacement method for signature 'NearestPeaksParam'
mzVsRtBalance(object) <- value
## S4 method for signature 'NearestPeaksParam'
absMz(object)
## S4 replacement method for signature 'NearestPeaksParam'
absMz(object) <- value
## S4 method for signature 'NearestPeaksParam'
absRt(object)
## S4 replacement method for signature 'NearestPeaksParam'
absRt(object) <- value
## S4 method for signature 'NearestPeaksParam'
kNN(object)
## S4 replacement method for signature 'NearestPeaksParam'
kNN(object) <- value
## S4 method for signature 'XCMSnExp,NearestPeaksParam'
groupChromPeaks(object, param, msLevel = 1L, add = FALSE)
|
sampleGroups |
A vector of the same length than samples defining the
sample group assignments (i.e. which samples belong to which sample
group). This parameter is mandatory for the |
mzVsRtBalance |
|
absMz |
|
absRt |
|
kNN |
|
object |
For For all other methods: a `NearestPeaksParam` object. |
value |
The value for the slot. |
param |
A |
msLevel |
|
add |
|
The NearestPeaksParam
function returns a
NearestPeaksParam
class instance with all of the settings
specified for peak alignment based on peak proximity.
For groupChromPeaks
: a XCMSnExp object with the results of the peak
grouping/correspondence step (i.e. the mz-rt features). These can be
accessed with the featureDefinitions()
method.
.__classVersion__,sampleGroups,mzVsRtBalance,absMz,absRt,kNN
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. All of the settings to the algorithm
can be passed with a NearestPeaksParam
object.
Katajamaa M, Miettinen J, Oresic M: MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 2006, 22:634-636.
The do_groupChromPeaks_nearest()
core API function.
featureDefinitions()
and featureValues()
for methods to access
peak grouping results (i.e. the features).
XCMSnExp for the object containing the results of the peak grouping.
Other peak grouping methods:
groupChromPeaks-density
,
groupChromPeaks-mzClust
,
groupChromPeaks()
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 | ## Create a NearestPeaksParam object
p <- NearestPeaksParam(kNN = 3)
p
## Load a test data set with detected peaks
data(faahko_sub)
## Update the path to the files for the local system
dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
res <- faahko_sub
## Disable parallel processing for this example
register(SerialParam())
head(chromPeaks(res))
## The number of peaks identified per sample:
table(chromPeaks(res)[, "sample"])
## Performing the peak grouping
p <- NearestPeaksParam()
res <- groupChromPeaks(res, param = p)
## The results from the peak grouping:
featureDefinitions(res)
## Using the featureValues method to extract a matrix with the intensities of
## the features per sample.
head(featureValues(res, value = "into"))
## The process history:
processHistory(res)
|
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