Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

Container for high-throughput mass-spectrometry assays and experimental metadata. This class is based on Biobase's "eSet" virtual class, with the notable exception that 'assayData' slot is an environment contain objects of class "Spectrum".

Objects from the Class

A virtual Class: No objects may be created from it. See "MSnExp" for instantiatable sub-classes.

Slots

assayData:: Object of class "environment" containing the MS spectra (see "Spectrum1" and "Spectrum2").
phenoData:: Object of class "AnnotatedDataFrame" containing experimenter-supplied variables describing sample (i.e the individual tags for an labelled MS experiment) See phenoData for more details.
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.
experimentData:: Object of class "MIAPE", containing details of experimental methods. See experimentData for more details.
protocolData:: Object of class "AnnotatedDataFrame" containing equipment-generated variables (inherited from "eSet"). See protocolData for more details.
processingData:: Object of class "MSnProcess" that records all processing.
.cache:: Object of class environment used to cache data. Under development.
.__classVersion__:: Object of class "Versions" describing the versions of the class.

Extends

Class "VersionedBiobase", directly. Class "Versioned", by class "VersionedBiobase", distance 2.

Methods

Methods defined in derived classes may override the methods described here.

[

signature(x = "pSet"): Subset current object and return object of same class.

[[

signature(x = "pSet"): Direct access to individual spectra.

$

signature(x = "pSet"): directly access a specific sample annotation column from the pData.

$<-

signature(x = "pSet"): replace or add a sample annotation column in the pData.

abstract

Access abstract in experimentData.

assayData

signature(object = "pSet"): Access the assayData slot. Returns an environment.

desciption

signature(x = "pSet"): Synonymous with experimentData.

dim

signature(x = "pSet"): Returns the dimensions of the phenoData slot.

experimentData

signature(x = "pSet"): Access details of experimental methods.

featureData

signature(x = "pSet"): Access the featureData slot.

fData

signature(x = "pSet"): Access feature data information.

featureNames

signature(x = "pSet"): Coordinate access of feature names (e.g spectra, peptides or proteins) in assayData slot.

fileNames

signature(object = "pSet"): Access file names in the processingData slot.

fromFile

signature(object = "pSet"): Access raw data file indexes (to be found in the processingData slot) from which the individual object's spectra where read from.

centroided

signature(object = "pSet"): Indicates whether individual spectra are centroided ('TRUE') of uncentroided ('FALSE'). Use centroided(object) <- value to update a whole experiment, ensuring that object and value have the same length.

smoothed

signature(object = "pSet"): Indicates whether individual spectra are smoothed ('TRUE') of unsmoothed ('FALSE'). Use smoothed(object) <- value to update a whole experiment, ensuring that object and value have the same length.

fvarMetadata

signature(x = "pSet"): Access metadata describing features reported in fData.

fvarLabels

signature(x = "pSet"): Access variable labels in featureData.

length

signature(x = "pSet"): Returns the number of features in the assayData slot.

notes

signature(x = "pSet"): Retrieve and unstructured notes associated with pSet in the experimentData slot.

pData

signature(x = "pSet"): Access sample data information.

pData<-

signature(x = "pSet", value): Replace sample data information with value, value being a data.frame.

phenoData

signature(x = "pSet"): Access the phenoData slot.

phenoData<-

signature(x = "pSet", value): Replace sample data information with value. value can be a data.frame or an AnnotatedDataFrame.

processingData

signature(object = "pSet"): Access the processingData slot.

protocolData

signature(x = "pSet"): Access the protocolData slot.

pubMedIds

signature(x = "pSet"): Access PMIDs in experimentData.

sampleNames

signature(x = "pSet"): Access sample names in phenoData. A replacement method is also available.

spectra

signature(x = "pSet", ...): Access the assayData slot, returning the features as a list. Additional arguments are currently ignored.

varMetadata

signature(x = "pSet"): Access metadata describing variables reported in pData.

varLabels

signature(x = "pSet"): Access variable labels in phenoData.

acquisitionNum

signature(object = "pSet"): Accessor for spectra acquisition numbers.

scanIndex

signature(object = "pSet"): Accessor for spectra scan indices.

collisionEnergy

signature(object = "pSet"): Accessor for MS2 spectra collision energies.

intensity

signature(object = "pSet", ...): Accessor for spectra instenities, returned as named list. Additional arguments are currently ignored.

msInfo

signature(object = "pSet"): Prints the MIAPE-MS meta-data stored in the experimentData slot.

msLevel

signature(object = "pSet"): Accessor for spectra MS levels.

mz

signature(object = "pSet", ...): Accessor for spectra M/Z values, returned as a named list. Additional arguments are currently ignored.

peaksCount

signature(object = "pSet"): Accessor for spectra preak counts.

peaksCount

signature(object = "pSet", scans = "numeric"): Accessor to scans spectra preak counts.

polarity

signature(object = "pSet"): Accessor for MS1 spectra polarities.

precursorCharge

signature(object = "pSet"): Accessor for MS2 precursor charges.

precursorIntensity

signature(object = "pSet"): Accessor for MS2 precursor intensity.

precursorMz

signature(object = "pSet"): Accessor for MS2 precursor M/Z values.

precAcquisitionNum

signature(object = "pSet"): Accessor for MS2 precursor scan numbers.

precScanNum

see precAcquisitionNum.

rtime

signature(object = "pSet", ...): Accessor for spectra retention times. Additional arguments are currently ignored.

tic

signature(object = "pSet", ...): Accessor for spectra total ion counts. Additional arguments are currently ignored.

ionCount

signature(object = "pSet"): Accessor for spectra total ion current.

header

signature(object = "pSet"): Returns a data frame containing all available spectra parameters (MSn only).

header

signature(object = "pSet", scans = "numeric"): Returns a data frame containing scans spectra parameters (MSn only).

spectrapply

spectrapply(signature(object = "pSet"), FUN = NULL, BPPARAM = bpparam(), ...): applies the function FUN to each spectrum passing additional parameters in ... to that function and return its results. For FUN = NULL it returns the list of spectra (same as a call to spectra). Parameter BPPARAM allows to specify how and if parallel processing should be enabled.

Returns a list with the result for each of spectrum.

isolationWindowLowerMz

isolationWindowLowerMz(object = "pSet"): return the lower m/z boundary for the isolation window. Note that this method is at present only available for OnDiskMSnExp objects.

isolationWindowUpperMz

isolationWindowUpperMz(object = "pSet"): return the upper m/z boundary for the isolation window. Note that this method is at present only available for OnDiskMSnExp objects.

Additional accessors for the experimental metadata (experimentData slot) are defined. See "MIAPE" for details.

References

The "eSet" class, on which pSet is based.

Author

Laurent Gatto

Examples

showClass("pSet")
#> Virtual Class "pSet" [package "MSnbase"]
#> 
#> Slots:
#>                                                                
#> Name:           assayData          phenoData        featureData
#> Class:        environment AnnotatedDataFrame AnnotatedDataFrame
#>                                                                
#> Name:      experimentData       protocolData     processingData
#> Class:              MIAxE AnnotatedDataFrame         MSnProcess
#>                                             
#> Name:              .cache  .__classVersion__
#> Class:        environment           Versions
#> 
#> Extends: "Versioned"
#> 
#> Known Subclasses: 
#> Class "MSnExp", directly
#> Class "OnDiskMSnExp", by class "MSnExp", distance 2, with explicit coerce