| MSnExp-class {MSnbase} | R Documentation |
The MSnExp class encapsulates data and meta-data for mass
spectrometry experiments, as described in the slots
section. Several data files (currently in mzXML) can be loaded
together with the function readMSData.
This class extends the virtual "pSet" class.
In version 1.19.12, the polarity slot had been added to the
"Spectrum" class (previously in
"Spectrum1"). Hence, "MSnExp" objects
created prior to this change will not be valid anymore, since all MS2
spectra will be missing the polarity slot. Object can be
appropriately updated using the updateObject method.
The feature variables in the feature data slot will depend on the
file. See also the documentation in the mzR package that parses
the raw data files and produces these data.
Objects can be created by calls of the form
new("MSnExp",...). However, it is preferred to use the
readMSData function that will read raw mass
spectrometry data to generate a valid "MSnExp" instance.
assayData:Object of class "environment"
containing the MS spectra (see "Spectrum1"
and "Spectrum2").
Slot is inherited from "pSet".
phenoData:Object of class
"NAnnotatedDataFrame" containing
experimenter-supplied variables describing sample (i.e the
individual tags for an labelled MS experiment)
See phenoData for more details.
Slot is inherited from "pSet".
featureData:Object of class
"AnnotatedDataFrame" containing variables
describing features (spectra in our case), e.g. identificaiton data,
peptide sequence, identification score,... (inherited from
"eSet"). See featureData for
more details.
Slot is inherited from "pSet".
experimentData:Object of class
"MIAPE", containing details of experimental
methods. See experimentData for more details.
Slot is inherited from "pSet".
protocolData:Object of class
"AnnotatedDataFrame" containing
equipment-generated variables (inherited from
"eSet"). See protocolData for
more details.
Slot is inherited from "pSet".
processingData:Object of class
"MSnProcess" that records all processing.
Slot is inherited from "pSet".
.__classVersion__:Object of class
"Versions" describing the versions of R,
the Biobase package, "pSet" and
MSnExp of the current instance.
Slot is inherited from "pSet".
Intended for developer use and debugging (inherited from
"eSet").
Class "pSet", directly.
Class "VersionedBiobase", by class "pSet", distance 2.
Class "Versioned", by class "pSet", distance 3.
See the "pSet" class for documentation on
accessors inherited from pSet, subsetting and general attribute
accession.
signature(object = "MSnExp"): Bins spectra.
See bin documentation for more details and examples.
signature(object = "MSnExp"): Removes unused 0
intensity data points. See clean documentation
for more details and examples.
signature(object1 = "Spectrum",
object2 = "missing"): Compares spectra. See
compareSpectra documentation for more details and
examples.
signature(object = "MSnExp", prec =
"numeric"): extracts spectra with precursor MZ value equal to
prec and returns an object of class 'MSnExp'.
See extractPrecSpectra documentation for more
details and examples.
signature(object = "MSnExp"): Performs the peak
picking to generate centroided spectra.
See pickPeaks documentation for more
details and examples.
signature(object = "MSnExp"): Estimates
the noise in all profile spectra of object. See
estimateNoise documentation for more details and
examples.
signature(x = "MSnExp", y = "missing"): Plots
the MSnExp instance. See plot.MSnExp
documentation for more details.
signature(object = "MSnExp", ...):
Plots retention time against precursor MZ for MSnExp
instances. See plot2d documentation for more
details.
signature(object = "MSnExp", ...):
Plots the density of parameters of interest.
instances. See plotDensity documentation for more
details.
signature(object = "MSnExp", ...):
Plots a histogram of the m/z difference betwee all of the highest
peaks of all MS2 spectra of an experiment.
See plotMzDelta documentation for more details.
signature(object = "MSnExp"): Performs
quantification for all the MS2 spectra of the MSnExp
instance. See quantify documentation for more
details. Also for OnDiskMSnExp objects.
signature(object = "MSnExp"): Removes
peaks lower that a threshold t. See
removePeaks documentation for more details and
examples.
signature(object = "MSnExp", ...):
Removes reporter ion peaks from all MS2 spectra of an
experiment. See removeReporters documentation for
more details and examples.
signature(x = "MSnExp"): Smooths spectra.
See smooth documentation for more details and examples.
signature(object = "MSnExp", ...):
Adds identification data to an experiment.
See addIdentificationData documentation for
more details and examples.
signature(object = "MSnExp", fcol =
"pepseq", keep = NULL): Removes non-identified features. See
removeNoId documentation for more details and
examples.
signature(object = "MSnExp",
fcol = "nprot"): Removes protein groups (or feature belong to
protein groups) with more than one member. The latter is defined
by extracting a feature variable (default is
"nprot"). Also removes non-identified features.
signature(object = "MSnExp", ...):
Prints a summary that lists the percentage of identified features per
file (called coverage).
signature(object = "MSnExp"): Displays object
content as text.
signature(object = "MSnExp", ...):
Returns the isolation window offsets for the MS2 spectra. See
isolationWindow for details.
signature(object = "MSnExp"): Trims the MZ
range of all the spectra of the MSnExp instance. See
trimMz documentation for more details and
examples.
isCentroided(object, k = 0.025, qtl = 0.9, verbose =
TRUE) A heuristic assessing if the spectra in the
object are in profile or centroided mode. The function
takes the qtlth quantile top peaks, then calculates the
difference between adjacent M/Z value and returns TRUE if
the first quartile is greater than k. (See
MSnbase:::.isCentroided for the code.) If verbose
(default), a table indicating mode for all MS levels is printed.
The function has been tuned to work for MS1 and MS2 spectra and data centroided using different peak picking algorithms, but false positives can occur. See https://github.com/lgatto/MSnbase/issues/131 for details. For whole experiments, where all MS1 and MS2 spectra are expected to be in the same, albeit possibly different modes, it is advised to assign the majority result for MS1 and MS2 spectra, rather than results for individual spectra. See an example below.
signature(object = "MSnExp", "data.frame"):
Coerces the MSnExp object to a four-column
data.frame with columns "file" (file index in
object), "rt" (retention time), "mz" (m/z
values) and "i" (intensity values).
signature(object = "MSnExp", "Spectra"):
Coerces the MSnExp object to a Spectra
object with all feature annotations added as metadata columns
(mcols).
Filtering and subsetting functions:
signature(object = "MSnExp", rt = "numeric",
msLevel. = "numeric"): Retains MS spectra of level
msLevel. with a retention times within rt[1] and
rt[2].
signature(object = "MSnExp", msLevel. =
"numeric"): Retains MS spectra of level msLevel..
signature(object = "MSnExp", mz = "numeric",
msLevel. = "numeric"). See filterMz for
details.
signature(object = "MSnExp", file): Retains
MS data of files matching the file index or file name provided
with parameter file.
signature(object = "MSnExp"):
Remove empty spectra from object (see isEmpty).
signature(object = "MSnExp",
acquisitionNum = "numeric"): Retain parent (e.g. MS1) and
children scans (e.g. MS2) of acquisitionNum. See
OnDiskMSnExp for an example.
signature(object = "MSnExp", f =
"factor"): split a MSnExp object by file into a
list of MSnExp objects given the grouping in
factor f.
Laurent Gatto <lg390@cam.ac.uk>
Information about the mzXML format as well converters from vendor specific formats to mzXML: http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML.
"pSet" and readMSData for loading
mzXML, mzData or mzML files to generate an
instance of MSnExp.
The "OnDiskMSnExp" manual page contains further
details and examples.
chromatogram to extract chromatographic data from a
MSnExp or OnDiskMSnExp object.
write for the function to write the data to mzML or
mzXML file(s).
mzxmlfile <- dir(system.file("extdata",package="MSnbase"),
pattern="mzXML",full.names=TRUE)
msnexp <- readMSData(mzxmlfile)
msnexp