pSet-class {MSnbase} | R Documentation |
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
"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.
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 'codeprocessingData' 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
.
signature(x = "pSet")
: Access the
phenoData
slot.
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.
Additional accessors for the experimental metadata
(experimentData
slot) are defined. See
"MIAPE"
for details.
Laurent Gatto <lg390@cam.ac.uk>
The "eSet"
class, on which pSet
is based.
"MSnExp"
for an instantiatable application of
pSet
.
showClass("pSet")