pSet-class {MSnbase} | R Documentation

## Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

### Description

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 `"NAnnotatedDataFrame"` 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 'codeprocessingData' 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`.

phenoData

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

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.

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

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>

### References

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

### See Also

`"MSnExp"` for an instantiatable application of `pSet`.

### Examples

    showClass("pSet")

[Package MSnbase version 2.4.2 Index]