R/AllGenerics.R, R/ChromBackend-functions.R, R/ChromBackend.R
ChromBackend.RdChromBackend is a virtual class that defines what different backends need
to provide to be used by the Chromatograms package and classes.
The backend should provide access to the chromatographic data which mainly consists of (paired) intensity and retention time values. Additional chromatographic metadata such as MS level and precursor and product m/z should also be provided.
Through their implementation different backends can be either optimized for minimal memory requirements or performance. Each backend needs to implemet data access methods listed in section Backend functions: below.
And example implementation and more details and descriptions are provided
in the Creating new ChromBackend classes for Chromatograms vignette.
chromData(object, ...)
chromData(object) <- value
chromIndex(object, ...)
chromNames(object, ...)
chromNames(object) <- value
chromVariables(object, ...)
mzMax(object, ...)
mzMax(object) <- value
mzMin(object, ...)
mzMin(object) <- value
precursorMzMin(object, ...)
precursorMzMin(object) <- value
precursorMzMax(object, ...)
precursorMzMax(object) <- value
productMzMax(object, ...)
productMzMax(object) <- value
productMzMin(object, ...)
productMzMin(object) <- value
selectChromVariables(object, ...)
coreChromVariables()
# S4 method for ChromBackend
[(x, i, j, ..., drop = FALSE)
# S4 method for ChromBackend
$(x, name)
# S4 method for ChromBackend
$(x, name) <- value
# S4 method for ChromBackend
backendInitialize(object, ...)
# S4 method for ChromBackend
chromData(object, columns = chromVariables(object))
# S4 method for ChromBackend
chromData(object) <- value
# S4 method for ChromBackend
selectChromVariables(object, chromVariables = chromVariables(object))
# S4 method for ChromBackend
peaksData(object, columns = c("rtime", "intensity"))
# S4 method for ChromBackend
peaksData(object) <- value
# S4 method for ChromBackend
backendMerge(object, ...)
# S4 method for ChromBackend
backendParallelFactor(object, ...)
# S4 method for list
backendMerge(object, ...)
# S4 method for ChromBackend
chromVariables(object)
# S4 method for ChromBackend
chromIndex(object, columns = chromVariables(object))
# S4 method for ChromBackend
collisionEnergy(object)
# S4 method for ChromBackend
collisionEnergy(object) <- value
# S4 method for ChromBackend
dataOrigin(object)
# S4 method for ChromBackend
dataOrigin(object) <- value
# S4 method for ChromBackend
dataStorage(object)
# S4 method for ChromBackend
dataStorage(object) <- value
# S4 method for ChromBackend
intensity(object)
# S4 method for ChromBackend
intensity(object) <- value
# S4 method for ChromBackend
isEmpty(x)
# S4 method for ChromBackend
isReadOnly(object)
# S4 method for ChromBackend
length(x)
# S4 method for ChromBackend
lengths(x)
# S4 method for ChromBackend
msLevel(object)
# S4 method for ChromBackend
msLevel(object) <- value
# S4 method for ChromBackend
mz(object)
# S4 method for ChromBackend
mz(object) <- value
# S4 method for ChromBackend
mzMax(object)
# S4 method for ChromBackend
mzMax(object) <- value
# S4 method for ChromBackend
mzMin(object)
# S4 method for ChromBackend
mzMin(object) <- value
# S4 method for ChromBackend
peaksVariables(object)
# S4 method for ChromBackend
precursorMz(object)
# S4 method for ChromBackend
precursorMz(object) <- value
# S4 method for ChromBackend
precursorMzMax(object)
# S4 method for ChromBackend
precursorMzMax(object) <- value
# S4 method for ChromBackend
precursorMzMin(object)
# S4 method for ChromBackend
precursorMzMin(object) <- value
# S4 method for ChromBackend
productMz(object)
# S4 method for ChromBackend
productMz(object) <- value
# S4 method for ChromBackend
productMzMax(object)
# S4 method for ChromBackend
productMzMax(object) <- value
# S4 method for ChromBackend
productMzMin(object)
# S4 method for ChromBackend
productMzMin(object) <- value
# S4 method for ChromBackend
rtime(object)
# S4 method for ChromBackend
rtime(object) <- value
# S4 method for ChromBackend,ANY
split(x, f, drop = FALSE, ...)
# S4 method for ChromBackend
filterDataOrigin(object, dataOrigin = character(), ...)
# S4 method for ChromBackend
filterDataStorage(object, dataStorage = character())
# S4 method for ChromBackend
filterMsLevel(object, msLevel = integer())
# S4 method for ChromBackend
filterMzRange(object, mz = numeric(), ...)
# S4 method for ChromBackend
filterMzValues(object, mz = numeric(), ppm = 20, tolerance = 0, ...)Object extending ChromBackend.
Additional arguments.
replacement value for <- methods. See individual
method description or expected data type.
Object extending ChromBackend.
For [: integer, logical or character to subset the object.
For [: ignored.
For [: not considered.
For $ and $<-: the name of the chromatogram variable to
return or set.
For chromData() accessor: optional character with column
names (chromatogram variables) that should be included in the
returned DataFrame. By default, all columns are returned.
For selectChromVariables(): character with the
names of the chromatogram variables to which the backend should be
subsetted.
factor defining the grouping to split x. See split().
For filterDataOrigin(): character to define which
chromatograms to keep.
For filterDataStorage(): character to define which
chromatograms to keep.
integer defining the MS level of the chromatograms to which
the function should be applied. For filterMsLevel(): the MS level to
which object should be subsetted.
For filterMzValues(): numeric with the m/z values of
chromatograms to keep. All chromatograms with their mz chromatogram
variable matching any of the values provided with this parameter are
retained. Parameters ppm and tolerance allow relaxed matching.
For filterMzRange(): numeric(2) defining the lower and upper
boundary of the m/z range. Chromatograms with their mz chromatogram
variable within this range are retained.
For filterMzValues(): m/z-relative acceptable difference (in
parts-per-million) for m/z values to be considered matching.
For filterMzValues(): largest acceptable absolute
difference in m/z values to consider them matching.
The core chromatogram variables are variables (metadata) that can/should
be provided by a backend. For each of these variables a value needs to be
returned, if none is defined, a missing value (of the correct data type)
should be returned. The names of the core variables are returned with the
chromVariables function.
For each core chromatogram variable a dedicated access method exists.
The coreChromVariables() function returns the core chromatogram variables
along with their expected (defined) data type.
The core chromatogram variables (in alphabetical order) are:
chromIndex: an integer with the index of the chromatogram in the
original source file (e.g. mzML file).
collisionEnergy: for SRM data, numeric with the collision energy of
the precursor.
dataOrigin: optional character with the origin of a chromatogram.
dataStorage: character defining where the data is (currently) stored.
intensity: NumericList with the intensity values of each chromatogram.
msLevel: integer defining the MS level of the data.
mz: optional numeric with the (target) m/z value for the
chromatographic data.
mzMin: optional numeric with the lower m/z value of the m/z range in
case the data (e.g. an extracted ion chromatogram EIC) was extracted from
a Spectra object.
mzMax: optional numeric with the upper m/z value of the m/z range.
precursorMz: for SRM data, numeric with the target m/z of the
precursor (parent).
precursorMzMin: for SRM data, optional numeric with the lower m/z of
the precursor's isolation window.
precursorMzMax: for SRM data, optional numeric with the upper m/z of
the precursor's isolation window.
productMz for SRM data, numeric with the target m/z of the
product ion.
productMzMin: for SRM data, optional numeric with the lower m/z of
the product's isolation window.
productMzMax: for SRM data, optional numeric with the upper m/z of
the product's isolation window.
rtime: NumericList with the retention times of each chromatogram.
retention times are expected to be increasingly sorted.
New backend classes must extend the base ChromBackend class and
implement the following mandatory methods:
backendInitialize(): initialises the backend. This method is
supposed to be called right after creating an instance of the
backend class and should prepare the backend.
Parameters can be defined freely for each backend, depending on what is
needed to initialize the backend. It is however suggested to also support
a parameter data that can be used to submit the full data as a
DataFrame to the backend. This would allow the backend to be also
usable for the setBackend() function from Chromatograms.
This method has to ensure to set the spectra variable dataStorage
correctly.
chromData(), chromData<-: gets or sets general chromatogram metadata
(annotation). chromData() returns a DataFrame, chromData<- expects
a DataFrame with the same number of rows as there are chromatograms in
object. Note that chromData() has to return the full data, i.e.
all core chromatogram variables and also the intensity and retention
time values (as a list or SimpleList in columns "intensity" and
"rtime". Read-only backends might not need to implement the
replacement method chromData<- (unless some internal caching mechanism
could be used).
peaksData(): returns a list of two-dimensional arrays (matrix or
data.frame) with the data (e.g. retention time - intensity pairs) from
each chromatogram. The length of the list is equal to the number of
chromatograms in object. For an empty chromatogram a matrix
with 0 rows and two columns (named "rtime" and "intensity") has to be
returned. The optional parameter columns, if supported by the backendallows to define which peak variables should be returned in each array. As default (minimum) columns"rtime"and"intensity"` have to be
provided.
peaksData<- replaces the peak data (retention time and intensity values)
of the backend. This method expects a list of two-dimensional arrays
(matrix or data.frame) with columns representing the peak variables.
All existing peaks data are expected to be replaced with these new values.
The length of the list has to match the number of spectra of object.
Note that only writeable backends need to support this method.
[: subset the backend. Only subsetting by element (row/i) is
allowed.
$, $<-: access or set/add a single chromatogram variable (column) in
the backend.
selectChromVariables(): reduce object retaining only specified
chromatogram variables.
backendMerge(): merges (combines) ChromBackend objects into a single
instance. All objects to be merged have to be of the same type.
Additional methods that might be implemented, but for which default implementations are already present are:
backendParallelFactor(): returns a factor defining an optimal
(preferred) way how the backend can be split for parallel processing
used for all peak data accessor or data manipulation functions.
The default implementation returns a factor of length 0 (factor())
providing thus no default splitting.
chromVariables(): returns a character vector with the
available chromatogram variables (columns, fields or attributes)
available in object. This should return all variables which
are present in object, also "intensity" and "rtime" (which are by
default not returned by the chromVariables,Chromatograms method).
chromIndex(): returns an integer vector with the index of the
chromatograms in the original source file.
collisionEnergy(), collisionEnergy<-: gets or sets the collision energy
for the precursor (for SRM data). collisionEnergy() returns a numeric
of length equal to the number of chromatograms in object.
dataOrigin(), dataOrigin<-: gets or sets the data origin variable.
dataOrigin() returns a character of length equal to the number of
chromatograms, dataOrigin<- expects a character of length equal
length(object).
dataStorage(), dataStorage<-: gets or sets the data storage variable.
dataStorage() returns a character of length equal to the number of
chromatograms in object, dataStorage<- expects a character of
length equal length(object). Note that missing values (NA_character_)
are not supported for dataStorage().
intensity(): gets the intensity values from the chromatograms. Returns
a NumericList() of numeric vectors (intensity values for each
chromatogram). The length of the list is equal to the number of
chromatograms in object.
intensity<-: replaces the intensity values. value has to be a list
(or NumericList()) of length equal to the number of chromatograms and
the number of values within each list element identical to the number of
data pairs in each chromatogram. Note that just writeable backends
need to support this method.
isReadOnly(): returns a logical(1) whether the backend is read
only or does allow also to write/update data.
isEmpty(): returns a logical of length equal to the number of
chromatograms with TRUE for chromatograms without any data pairs.
length(): returns the number of chromatograms in the object.
lengths(): returns the number of data pairs (retention time and intensity
values) per chromatogram.
msLevel(): gets the chromatogram's MS level. Returns an integer
vector (of length equal to the number of chromatograms) with the MS
level for each chromatogram (or NA_integer_ if not available).
mz(),mz<-: gets or sets the m/z value of the chromatograms. mz()
returns a numeric of length equal to the number of chromatograms in object, mz<- expects a numeric of length length(object).
mzMax(),mzMax<-: gets or sets the upper m/z of the mass-to-charge
range from which a chromatogram contains signal (e.g. if the chromatogram
was extracted from MS data in spectra format and a m/z range was provided).
mzMax() returns a numeric of length equal to the number of
chromatograms in object, mzMax<- expects a numeric of length equal
to the number of chromatograms in object.
mzMin(),mzMin<-: gets or sets the lower m/z of the mass-to-charge range
from which a chromatogram contains signal (e.g. if the chromatogram
was extracted from MS data in spectra format and a m/z range was provided).
mzMin() returns a numeric of length equal to the number of
chromatograms in object, mzMin<- expects a numeric of length equal
to the number of chromatograms in object.
peaksVariables(): lists the available data variables for the
chromatograms. Default peak variables are "rtime" and "intensity"
(which all backends need to support and provide), but some backends
might provide additional variables.
Variables listed by this function are expected to be returned (if
requested) by the peaksData() function.
precursorMz(),precursorMz<-: gets or sets the (target) m/z of the
precursor (for SRM data). precursorMz() returns a numeric of length
equal to the number of chromatograms in object. precursorMz<- expects
a numeric of length equal to the number of chromatograms.
precursorMzMin(),precursorMzMax(),productMzMin(), productMzMax():
gets the lower and upper margin for the precursor or product isolation
windows. These functions might return the value of productMz() if the
respective minimal or maximal m/z values are not defined in object.
productMz(),productMz<-: gets or sets the (target) m/z of the
product (for SRM data). productMz() returns a numeric of length
equal to the number of chromatograms in object. productMz<- expects
a numeric of length equal to the number of chromatograms.
rtime(): gets the retention times from the chromatograms. returns a
NumericList() of numeric vectors (retention times for each
chromatogram). The length of the returned list is equal to the number of
chromatograms in object.
rtime<-: replaces the retention times. value has to be a list (or
NumericList()) of length equal to the number of chromatograms and the
number of values within each list element identical to the number of
data pairs in each chromatogram. Note that just writeable backends support
this method.
split(): splits the backend into a list of backends (depending on
parameter f). The default method for ChromBackend uses
split.default(), thus backends extending ChromBackend don't
necessarily need to implement this method.
Filter methods:
filterDataOrigin(): filters the object retaining chromatograms matching
any of the provided dataOrigin. Parameter dataOrigin has to be of
type character and needs to match exactly the data origin value of the
chromatograms to subset.
filterDataOrigin() should return the data ordered by the provided
dataOrigin parameter, i.e. if dataOrigin = c("2", "1") was provided,
the chromatograms in the resulting object should be ordered accordingly
(first chromatogram from data origin "2" and then from "1").
filterDataStorage(): filters the object retaining chromatograms matching
any of the provided dataStorage. Parameter dataStorage has to be
of type character and needs to match exactly the data storage value of
the chromatograms to subset.
filterDataStorage() should return the data ordered by the provided
dataStorage parameter, i.e. if dataStorage = c("2", "1") was
provided, the chromatograms in the resulting object should be ordered
accordingly (first chromatogram from data storage "2" and then from
"1").
filterMsLevel(): retains chromatograms of MS level msLevel().
filterMzRange(): retains chromatograms with their m/z within the
provided m/z range.
filterMzValues(): retains chromatograms with their m/z matching any of
the provided m/z values (given the provided acceptable differences defined
by parameters tolerance and ppm.
Backends extending ChromBackend must implement all of its methods
(listed above). A guide to create new backend classes is provided as a
dedicated vignette. Additional information and an example for a backend
implementation is provided in the respective vignette.
## Create a simple backend implementation
ChromBackendDummy <- setClass("ChromBackendDummy",
contains = "ChromBackend")