pSet-class.Rd
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"
.
A virtual Class: No objects may be created from it.
See "MSnExp"
for instantiatable sub-classes.
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.
Class "VersionedBiobase"
, directly.
Class "Versioned"
, by class "VersionedBiobase", distance 2.
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
.
Access abstract in experimentData
.
signature(object = "pSet")
: Access the
assayData
slot. Returns an environment
.
signature(x = "pSet")
: Synonymous with
experimentData.
signature(x = "pSet")
: Returns the dimensions of
the phenoData
slot.
signature(x = "pSet")
: Access details
of experimental methods.
signature(x = "pSet")
: Access the
featureData
slot.
signature(x = "pSet")
: Access feature data
information.
signature(x = "pSet")
: Coordinate access
of feature names (e.g spectra, peptides or proteins) in
assayData
slot.
signature(object = "pSet")
: Access file
names in the processingData
slot.
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.
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.
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.
signature(x = "pSet")
: Access metadata
describing features reported in fData
.
signature(x = "pSet")
: Access variable
labels in featureData
.
signature(x = "pSet")
: Returns the number of
features in the assayData
slot.
signature(x = "pSet")
: Retrieve and
unstructured notes associated with pSet
in the
experimentData
slot.
signature(x = "pSet")
: Access sample data
information.
signature(x = "pSet", value)
: Replace sample data
information with value
, value being a data.frame
.
signature(x = "pSet")
: Access the
phenoData
slot.
signature(x = "pSet", value)
: Replace
sample data information with value
. value
can be a
data.frame
or an AnnotatedDataFrame
.
signature(object = "pSet")
: Access the
processingData
slot.
signature(x = "pSet")
: Access the
protocolData
slot.
signature(x = "pSet")
: Access PMIDs in
experimentData
.
signature(x = "pSet")
: Access sample names
in phenoData
. A replacement method is also available.
signature(x = "pSet", ...)
: Access the
assayData
slot, returning the features as a list
.
Additional arguments are currently ignored.
signature(x = "pSet")
: Access metadata
describing variables reported in pData
.
signature(x = "pSet")
: Access variable
labels in phenoData
.
signature(object = "pSet")
: Accessor
for spectra acquisition numbers.
signature(object = "pSet")
: Accessor
for spectra scan indices.
signature(object = "pSet")
: Accessor
for MS2 spectra collision energies.
signature(object = "pSet", ...)
: Accessor
for spectra instenities, returned as named list. Additional
arguments are currently ignored.
signature(object = "pSet")
: Prints the MIAPE-MS
meta-data stored in the experimentData
slot.
signature(object = "pSet")
: Accessor for
spectra MS levels.
signature(object = "pSet", ...)
: Accessor for spectra
M/Z values, returned as a named list. Additional arguments are
currently ignored.
signature(object = "pSet")
: Accessor for
spectra preak counts.
signature(object = "pSet", scans =
"numeric")
: Accessor to scans
spectra preak counts.
signature(object = "pSet")
: Accessor for MS1
spectra polarities.
signature(object = "pSet")
: Accessor
for MS2 precursor charges.
signature(object = "pSet")
: Accessor
for MS2 precursor intensity.
signature(object = "pSet")
: Accessor
for MS2 precursor M/Z values.
signature(object = "pSet")
: Accessor
for MS2 precursor scan numbers.
see precAcquisitionNum
.
signature(object = "pSet", ...)
: Accessor for spectra
retention times. Additional arguments are currently ignored.
signature(object = "pSet", ...)
: Accessor for spectra
total ion counts. Additional arguments are currently ignored.
signature(object = "pSet")
: Accessor for spectra
total ion current.
signature(object = "pSet")
: Returns a data
frame containing all available spectra parameters (MSn only).
signature(object = "pSet", scans = "numeric")
:
Returns a data frame containing scans
spectra parameters
(MSn only).
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(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(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.
The "eSet"
class, on which pSet
is based.
"MSnExp"
for an instantiatable application of
pSet
.
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