XCMSnExp data manipulation methods inherited from MSnbase
Source:R/methods-XCMSnExp.R
XCMSnExp-inherited-methods.Rd
The methods listed on this page are XCMSnExp
methods inherited from its parent, the
OnDiskMSnExp
class from the MSnbase
package, that alter the raw data or are related to data subsetting. Thus
calling any of these methods causes all xcms
pre-processing
results to be removed from the XCMSnExp
object to ensure
its data integrity.
bin
: allows to bin spectra. See
bin
documentation in the MSnbase
package for more
details and examples.
clean
: removes unused 0
intensity data
points. See clean
documentation in the MSnbase
package
for details and examples.
filterAcquisitionNum
: filters the
XCMSnExp
object keeping only spectra with the provided
acquisition numbers. See filterAcquisitionNum
for
details and examples.
The normalize
method performs basic normalization of
spectra intensities. See normalize
documentation
in the MSnbase
package for details and examples.
The pickPeaks
method performs peak picking. See
pickPeaks
documentation for details and examples.
The removePeaks
method removes mass peaks (intensities)
lower than a threshold. Note that these peaks refer to mass
peaks, which are different to the chromatographic peaks detected and
analyzed in a metabolomics experiment! See
removePeaks
documentation for details and
examples.
The smooth
method smooths spectra. See
smooth
documentation in MSnbase
for details and
examples.
Usage
# S4 method for class 'XCMSnExp'
bin(x, binSize = 1L, msLevel.)
# S4 method for class 'XCMSnExp'
clean(object, all = FALSE, verbose = FALSE, msLevel.)
# S4 method for class 'XCMSnExp'
filterAcquisitionNum(object, n, file)
# S4 method for class 'XCMSnExp'
normalize(object, method = c("max", "sum"), ...)
# S4 method for class 'XCMSnExp'
pickPeaks(
object,
halfWindowSize = 3L,
method = c("MAD", "SuperSmoother"),
SNR = 0L,
...
)
# S4 method for class 'XCMSnExp'
removePeaks(object, t = "min", verbose = FALSE, msLevel.)
# S4 method for class 'XCMSnExp'
smooth(
x,
method = c("SavitzkyGolay", "MovingAverage"),
halfWindowSize = 2L,
verbose = FALSE,
...
)
Arguments
- x
XCMSnExp
orOnDiskMSnExp
object.- binSize
numeric(1)
defining the size of a bin (in Dalton).- msLevel.
For
bin
,clean
,filterMsLevel
,removePeaks
:numeric(1)
defining the MS level(s) to which operations should be applied or to which the object should be subsetted.- object
XCMSnExp
orOnDiskMSnExp
object.- all
For
clean
:logical(1)
, ifTRUE
all zeros are removed.- verbose
logical(1)
whether progress information should be displayed.- n
For
filterAcquisitionNum
:integer
defining the acquisition numbers of the spectra to which the data set should be sub-setted.- file
For
filterAcquisitionNum
:integer
defining the file index within the object to subset the object by file.- method
For
normalize
:character(1)
specifying the normalization method. Seenormalize
in theMSnbase
package for details. ForpickPeaks
:character(1)
defining the method. SeepickPeaks
for options. Forsmooth
:character(1)
defining the method. Seesmooth
in theMSnbase
package for options and details.- ...
Optional additional arguments.
- halfWindowSize
For
pickPeaks
andsmooth
:integer(1)
defining the window size for the peak picking. SeepickPeaks
andsmooth
in theMSnbase
package for details and options.- SNR
For
pickPeaks
:numeric(1)
defining the signal to noise ratio to be considered. SeepickPeaks
documentation for details.- t
For
removePeaks
: either anumeric(1)
or"min"
defining the threshold (method) to be used. SeeremovePeaks
for details.
See also
XCMSnExp-filter
for methods to filter and subset
XCMSnExp
objects.
XCMSnExp
for base class documentation.
OnDiskMSnExp
for the documentation of the
parent class.