MsBackend: Mass spectrometry data backends

In rformassspectrometry/Spectra: Spectra Infrastructure for Mass Spectrometry Data

Mass spectrometry data backends

Description

Note that the classes described here are not meant to be used directly by the end-users and the material in this man page is aimed at package developers.

MsBackend is a virtual class that defines what each different backend needs to provide. MsBackend objects provide access to mass spectrometry data. Such backends can be classified into in-memory or on-disk backends, depending on where the data, i.e spectra (m/z and intensities) and spectra annotation (MS level, charge, polarity, ...) are stored.

Typically, in-memory backends keep all data in memory ensuring fast data access, while on-disk backends store (parts of) their data on disk and retrieve it on demand.

The Backend functions and implementation notes for new backend classes section documents the API that a backend must implement.

Currently available backends are:

• MsBackendMemory and MsBackendDataFrame: store all data in memory. The MsBackendMemory is optimized for accessing and processing the peak data (i.e. the numerical matrices with the m/z and intensity values) while the MsBackendDataFrame keeps all data in a DataFrame.

• MsBackendMzR: stores the m/z and intensities on-disk in raw data files (typically mzML or mzXML) and the spectra annotation information (header) in memory in a DataFrame. This backend requires the mzR package.

• MsBackendHdf5Peaks: stores the m/z and intensities on-disk in custom hdf5 data files and the remaining spectra variables in memory (in a DataFrame). This backend requires the rhdf5 package.

See below for more details about individual backends.

Usage

## S4 method for signature 'MsBackend'
backendBpparam(object, BPPARAM = bpparam())

## S4 method for signature 'MsBackend'
backendInitialize(object, ...)

## S4 method for signature 'list'
backendMerge(object, ...)

## S4 method for signature 'MsBackend'
backendMerge(object, ...)

## S4 method for signature 'MsBackend'
backendParallelFactor(object, ...)

## S4 method for signature 'MsBackend'
export(object, ...)

## S4 method for signature 'MsBackend'
acquisitionNum(object)

## S4 method for signature 'MsBackend'
peaksData(object, columns = c("mz", "intensity"))

## S4 method for signature 'MsBackend'
peaksVariables(object)

## S4 method for signature 'MsBackend,dataframeOrDataFrameOrmatrix'
cbind2(x, y = data.frame(), ...)

## S4 method for signature 'MsBackend'
centroided(object)

## S4 replacement method for signature 'MsBackend'
centroided(object) <- value

## S4 method for signature 'MsBackend'
collisionEnergy(object)

## S4 replacement method for signature 'MsBackend'
collisionEnergy(object) <- value

## S4 method for signature 'MsBackend'
dataOrigin(object)

## S4 replacement method for signature 'MsBackend'
dataOrigin(object) <- value

## S4 method for signature 'MsBackend'
dataStorage(object)

## S4 replacement method for signature 'MsBackend'
dataStorage(object) <- value

## S4 method for signature 'MsBackend'
dropNaSpectraVariables(object)

## S4 method for signature 'MsBackend,ANY'
extractByIndex(object, i)

## S4 method for signature 'MsBackend,missing'
extractByIndex(object, i)

## S4 method for signature 'MsBackend'
filterAcquisitionNum(object, n, file, ...)

## S4 method for signature 'MsBackend'
filterDataOrigin(object, dataOrigin = character())

## S4 method for signature 'MsBackend'
filterDataStorage(object, dataStorage = character())

## S4 method for signature 'MsBackend'
filterEmptySpectra(object, ...)

## S4 method for signature 'MsBackend'
filterIsolationWindow(object, mz = numeric(), ...)

## S4 method for signature 'MsBackend'
filterMsLevel(object, msLevel = integer())

## S4 method for signature 'MsBackend'
filterPolarity(object, polarity = integer())

## S4 method for signature 'MsBackend'
filterPrecursorMzRange(object, mz = numeric())

## S4 method for signature 'MsBackend'
filterPrecursorMz(object, mz = numeric())

## S4 method for signature 'MsBackend'
filterPrecursorMzValues(object, mz = numeric(), ppm = 20, tolerance = 0)

## S4 method for signature 'MsBackend'
filterPrecursorCharge(object, z = integer())

## S4 method for signature 'MsBackend'
filterPrecursorScan(object, acquisitionNum = integer(), f = dataOrigin(object))

## S4 method for signature 'MsBackend'
filterRanges(
  object,
  spectraVariables = character(),
  ranges = numeric(),
  match = c("all", "any")
)

## S4 method for signature 'MsBackend'
filterRt(object, rt = numeric(), msLevel. = uniqueMsLevels(object))

## S4 method for signature 'MsBackend'
filterValues(
  object,
  spectraVariables = character(),
  values = numeric(),
  ppm = 0,
  tolerance = 0,
  match = c("all", "any")
)

## S4 method for signature 'MsBackend'
intensity(object)

## S4 replacement method for signature 'MsBackend'
intensity(object) <- value

## S4 method for signature 'MsBackend'
ionCount(object)

## S4 method for signature 'MsBackend'
isCentroided(object, ...)

## S4 method for signature 'MsBackend'
isEmpty(x)

## S4 method for signature 'MsBackend'
isolationWindowLowerMz(object)

## S4 replacement method for signature 'MsBackend'
isolationWindowLowerMz(object) <- value

## S4 method for signature 'MsBackend'
isolationWindowTargetMz(object)

## S4 replacement method for signature 'MsBackend'
isolationWindowTargetMz(object) <- value

## S4 method for signature 'MsBackend'
isolationWindowUpperMz(object)

## S4 replacement method for signature 'MsBackend'
isolationWindowUpperMz(object) <- value

## S4 method for signature 'MsBackend'
isReadOnly(object)

## S4 method for signature 'MsBackend'
length(x)

## S4 method for signature 'MsBackend'
msLevel(object)

## S4 replacement method for signature 'MsBackend'
msLevel(object) <- value

## S4 method for signature 'MsBackend'
mz(object)

## S4 replacement method for signature 'MsBackend'
mz(object) <- value

## S4 method for signature 'MsBackend'
lengths(x, use.names = FALSE)

## S4 method for signature 'MsBackend'
polarity(object)

## S4 replacement method for signature 'MsBackend'
polarity(object) <- value

## S4 method for signature 'MsBackend'
precScanNum(object)

## S4 method for signature 'MsBackend'
precursorCharge(object)

## S4 method for signature 'MsBackend'
precursorIntensity(object)

## S4 method for signature 'MsBackend'
precursorMz(object)

## S4 replacement method for signature 'MsBackend'
precursorMz(object, ...) <- value

## S4 replacement method for signature 'MsBackend'
peaksData(object) <- value

## S4 method for signature 'MsBackend'
reset(object)

## S4 method for signature 'MsBackend'
rtime(object)

## S4 replacement method for signature 'MsBackend'
rtime(object) <- value

## S4 method for signature 'MsBackend'
scanIndex(object)

## S4 method for signature 'MsBackend'
selectSpectraVariables(object, spectraVariables = spectraVariables(object))

## S4 method for signature 'MsBackend'
smoothed(object)

## S4 replacement method for signature 'MsBackend'
smoothed(object) <- value

## S4 method for signature 'MsBackend'
spectraData(object, columns = spectraVariables(object))

## S4 replacement method for signature 'MsBackend'
spectraData(object) <- value

## S4 method for signature 'MsBackend'
spectraNames(object)

## S4 replacement method for signature 'MsBackend'
spectraNames(object) <- value

## S4 method for signature 'MsBackend'
spectraVariables(object)

## S4 method for signature 'MsBackend,ANY'
split(x, f, drop = FALSE, ...)

## S4 method for signature 'MsBackend'
supportsSetBackend(object, ...)

## S4 method for signature 'MsBackend'
tic(object, initial = TRUE)

## S4 method for signature 'MsBackend'
x[i, j, ..., drop = FALSE]

## S4 method for signature 'MsBackend'
x$name

## S4 replacement method for signature 'MsBackend'
x$name <- value

## S4 method for signature 'MsBackend'
x[[i, j, ...]]

## S4 replacement method for signature 'MsBackend'
x[[i, j, ...]] <- value

## S4 method for signature 'MsBackend'
uniqueMsLevels(object, ...)

## S4 method for signature 'MsBackend'
dataStorageBasePath(object)

## S4 replacement method for signature 'MsBackend'
dataStorageBasePath(object) <- value

MsBackendDataFrame()

## S4 method for signature 'MsBackendDataFrame'
backendInitialize(object, data, peaksVariables = c("mz", "intensity"), ...)

MsBackendHdf5Peaks()

MsBackendMemory()

## S4 method for signature 'MsBackendMemory'
backendInitialize(object, data, peaksVariables = c("mz", "intensity"), ...)

MsBackendMzR()

Arguments

object	Object extending MsBackend.
BPPARAM	for backendBpparam(): parameter object from the BiocParallel package defining the parallel processing setup. Defaults to BPPARAM = bpparam(). See BiocParallel::bpparam() for more information.
...	Additional arguments.
columns	For spectraData() accessor: optional character with column names (spectra variables) that should be included in the returned DataFrame. By default, all columns are returned. For peaksData() accessor: optional character with requested columns in the individual matrix of the returned list. Defaults to peaksVariables(object) and depends on what peaks variables the backend provides.
x	Object extending MsBackend.
y	For cbind2(): A data.frame or DataFrame with the spectra variables to be added to the backend. The number of rows of y and their order have to match the number of spectra and their order in x.
value	replacement value for ⁠<-⁠ methods. See individual method description or expected data type.
i	For [: integer, logical or character to subset the object.
n	for filterAcquisitionNum(): integer with the acquisition numbers to filter for.
file	For filterFile(): index or name of the file(s) to which the data should be subsetted. For export(): character of length 1 or equal to the number of spectra.
dataOrigin	For filterDataOrigin(): character to define which spectra to keep. For filterAcquisitionNum(): optionally specify if filtering should occur only for spectra of selected dataOrigin.
dataStorage	For filterDataStorage(): character to define which spectra to keep. For filterAcquisitionNum(): optionally specify if filtering should occur only for spectra of selected dataStorage.
mz	For filterIsolationWindow(): numeric(1) with the m/z value to filter the object. For filterPrecursorMzRange(): numeric(2) with the lower and upper m/z boundary. For filterPrecursorMzValues(): numeric with the m/z value(s) to filter the object.
msLevel	integer defining the MS level of the spectra to which the function should be applied. For filterMsLevel(): the MS level to which object should be subsetted.
polarity	For filterPolarity(): integer specifying the polarity to to subset object.
ppm	For filterPrecursorMzValues(): numeric(1) with the m/z-relative maximal acceptable difference for a m/z to be considered matching. See MsCoreUtils::closest() for details. For filterValues(): numeric of any length allowing to define a maximal accepted difference between user input values and the spectraVariables values. If it is not equal to the length of the value provided with parameter spectraVariables, ppm[1] will be recycled.
tolerance	For filterPrecursorMzValues(): numeric(1) with the maximal absolute acceptable difference for a m/z value to be considered matching. See MsCoreUtils::closest() for details. For filterValues(): numeric accepted tolerance between the values and the spectra variables. Defaults to tolerance = 0. If it is not equal to the length of the value provided with parameter spectraVariables, tolerance[1] will be recycled.
z	For filterPrecursorCharge(): integer() with the precursor charges to be used as filter.
acquisitionNum	for filterPrecursorScan(): integer with the acquisition number of the spectra to which the object should be subsetted.
f	factor defining the grouping to split x. See split(). For filterPrecursorScan(): factor defining from which original data files the spectra derive to avoid selecting spectra from different samples/files. Defaults to f = dataOrigin(object).
spectraVariables	For selectSpectraVariables(): character with the names of the spectra variables to which the backend should be subsetted. For filterRanges() and filterValues(): character vector specifying the column(s) from spectraData(object) on which to filter the data and that correspond to the the names of the spectra variables that should be used for the filtering.
ranges	for filterRanges(): A numeric vector of paired values (upper and lower boundary) that define the ranges to filter the object. These paired values need to be in the same order as the spectraVariables parameter (see below).
match	For filterRanges() and filterValues(): character(1) defining whether the condition has to match for all provided ranges/values (match = "all"; the default), or for any of them (match = "any") for spectra to be retained.
rt	for filterRt(): numeric(2) defining the retention time range to be used to subset/filter object.
msLevel.	same as msLevel above.
values	For filterValues(): A numeric vector that define the values to filter the object. values needs to be of same length than parameter spectraVariables and in the same order.
use.names	For lengths(): whether spectrum names should be used.
drop	For [: not considered.
initial	For tic(): logical(1) whether the initially reported total ion current should be reported, or whether the total ion current should be (re)calculated on the actual data (initial = FALSE).
j	For [: not supported.
name	For $ and ⁠$<-⁠: the name of the spectra variable to return or set.
data	For backendInitialize(): DataFrame with spectrum metadata/data. This parameter can be empty for MsBackendMzR backends but needs to be provided for MsBackendDataFrame backends.
peaksVariables	For backendInitialize() for MsBackendMemory: character specifying which of the columns of the provided data contain peaks variables (i.e. information for individual mass peaks). Defaults to peaksVariables = c("mz", "intensity"). "mz" and "intensity" should always be specified.

Value

See documentation of respective function.

Implementation notes

Backends extending MsBackend must implement all of its methods (listed above). Developers of new MsBackends should follow the MsBackendMemory implementation. To ensure a new implementation being conform with the MsBackend definition, developers should included test suites provided by this package in their unit test setup. For that a variable be should be created in the package's "testthat.R" file that represents a (initialized) instance of the developed backend. Then the path to the test suites should be defined with test_suite <- system.file("test_backends", "test_MsBackend", package = "Spectra") followed by test_dir(test_suite) to run all test files in that directory. Individual unit test files could be run with test_file(file.path(test_suite, "test_spectra_variables.R"), stop_on_failure = TRUE) (note that without stop_on_failure = TRUE tests would fail silently) . Adding this code to the packages "testthat.R" file ensures that all tests checking the validity of an MsBackend instance defined in the Spectra package are also run on the newly develped backend class.

The MsBackend defines the following slots:

• ⁠@readonly⁠: logical(1) whether the backend supports writing/replacing of m/z or intensity values.

Backends extending MsBackend must implement all of its methods (listed above). Developers of new MsBackends should follow the MsBackendDataFrame implementation.

The MsBackendCached() backend provides a caching mechanism to allow read only backends to add or change spectra variables. This backend shouldn't be used on its own, but is meant to be extended. See MsBackendCached() for details.

The MsBackend defines the following slots:

• ⁠@readonly⁠: logical(1) whether the backend supports writing/replacing of m/z or intensity values.

Backend functions

New backend classes must extend the base MsBackend class will have to implement some of the following methods (see the MsBackend vignette for detailed description and examples):

• [: subset the backend. Only subsetting by element (row/i) is allowed. Parameter i should support integer indices and logical and should throw an error if i is out of bounds. The MsCoreUtils::i2index could be used to check the input i. For i = integer() an empty backend should be returned. Implementation of this method is optional, as the default calls the extractByIndex() method (which has to be implemented as the main subsetting method).

• $, ⁠$<-⁠: access or set/add a single spectrum variable (column) in the backend. Using a value of NULL should allow deleting the specified spectra variable. An error should be thrown if the spectra variable is not available.

• [[, ⁠[[<-⁠: access or set/add a single spectrum variable (column) in the backend. The default implementation uses $, thus these methods don't have to be implemented for new classes extending MsBackend.

• acquisitionNum(): returns the acquisition number of each spectrum. Returns an integer of length equal to the number of spectra (with NA_integer_ if not available).

• backendBpparam(): return the parallel processing setup supported by the backend class. This function can be used by any higher level function to evaluate whether the provided parallel processing setup (or the default one returned by bpparam()) is supported by the backend. Backends not supporting parallel processing (e.g. because they contain a connection to a database that can not be shared across processes) should extend this method to return only SerialParam() and hence disable parallel processing for (most) methods and functions. See also backendParallelFactor() for a function to provide a preferred splitting of the backend for parallel processing.

• backendInitialize(): initialises the backend. This method is supposed to be called rights after creating an instance of the backend class and should prepare the backend (e.g. set the data for the memory backend or read the spectra header data for the MsBackendMzR 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 spectra data as a DataFrame to the backend. This would allow the backend to be also usable for the setBackend() function from Spectra. Note that eventually (for read-only backends) also the supportsSetBackend method would need to be implemented to return TRUE. The backendInitialize() method has also to ensure to correctly set spectra variable dataStorage.

• backendMerge(): merges (combines) MsBackend objects into a single instance. All objects to be merged have to be of the same type (e.g. MsBackendDataFrame()).

• 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. backendParallelFactor() for MsBackendMzR on the other hand returns factor(dataStorage(object)) hence suggesting to split the object by data file.

• backendRequiredSpectraVariables(): returns a character with spectra variable names that are mandatory for a specific backend. The default returns an empty character(). The implementation for MsBackendMzR returns c("dataStorage", "scanIndex") as these two spectra variables are required to load the MS data on-the-fly. This method needs only to be implemented if a backend requires specific variables to be defined.

• dataOrigin(): gets a character of length equal to the number of spectra in object with the data origin of each spectrum. This could e.g. be the mzML file from which the data was read.

• dataStorage(): gets a character of length equal to the number of spectra in object with the data storage of each spectrum. Note that missing values (NA_character_) are not supported for dataStorage.

• dataStorageBasePath(), ⁠dataStorageBasePath<-: gets or sets the common *base* path of the directory containing all data files. If supported, the function is expected to return (or accept) a ⁠character⁠of length 1. Most backends (such as for example the⁠MsBackendMemory⁠will not support this function and⁠dataStorageBasePath()⁠will return⁠NA_character_⁠. For ⁠MsBackendMzR⁠, this function allows to get or change the path to the directory containing the original data files, which is required if e.g. a serialized ⁠MsBackendMzR' instance gets copied to another computer or file system.

• dropNaSpectraVariables(): removes spectra variables (i.e. columns in the object's spectraData that contain only missing values (NA). Note that while columns with only NAs are removed, a spectraData() call after dropNaSpectraVariables() might still show columns containing NA values for core spectra variables.

• cbind2(): allows to appends multiple new spectra variables to the backend at once. The values for the new spectra variables have to be in the same order as the spectra in x. Replacing existing spectra variables is not supported through this function. For a more controlled way of adding spectra variables, the joinSpectraData() should be used.

• centroided(), ⁠centroided<-⁠: gets or sets the centroiding information of the spectra. centroided() returns a logical vector of length equal to the number of spectra with TRUE if a spectrum is centroided, FALSE if it is in profile mode and NA if it is undefined. See also isCentroided() for estimating from the spectrum data whether the spectrum is centroided. value for ⁠centroided<-⁠ is either a single logical or a logical of length equal to the number of spectra in object.

• collisionEnergy(), ⁠collisionEnergy<-⁠: gets or sets the collision energy for all spectra in object. collisionEnergy() returns a numeric with length equal to the number of spectra (NA_real_ if not present/defined), ⁠collisionEnergy<-⁠ takes a numeric of length equal to the number of spectra in object.

• export(): exports data from a Spectra class to a file. This method is called by the ⁠export,Spectra⁠ method that passes itself as a second argument to the function. The ⁠export,MsBackend⁠ implementation is thus expected to take a Spectra class as second argument from which all data is exported. Taking data from a Spectra class ensures that also all eventual data manipulations (cached in the Spectra's lazy evaluation queue) are applied prior to export - this would not be possible with only a MsBackend class. An example implementation is the export() method for the MsBackendMzR backend that supports export of the data in mzML or mzXML format. See the documentation for the MsBackendMzR class below for more information.

• extractByIndex(): function to subset a backend to selected elements defined by the provided index. Similar to [, this method should allow extracting (or to subset) the data in any order. In contrast to [, however, i is expected to be an integer (while [ should also support logical and eventually character). While being apparently redundant to [, this methods avoids package namespace errors/problems that can result in implementations of [ being not found by R (which can happen sometimes in parallel processing using the BiocParallel::SnowParam()). This method is used internally by Spectra to extract/subset its backend. Implementation of this method is mandatory.

• filterAcquisitionNum(): filters the object keeping only spectra matching the provided acquisition numbers (argument n). If dataOrigin or dataStorage is also provided, object is subsetted to the spectra with an acquisition number equal to n in spectra with matching dataOrigin or dataStorage values retaining all other spectra.

• filterDataOrigin(): filters the object retaining spectra matching the provided dataOrigin. Parameter dataOrigin has to be of type character and needs to match exactly the data origin value of the spectra to subset. filterDataOrigin() should return the data ordered by the provided dataOrigin parameter, i.e. if dataOrigin = c("2", "1") was provided, the spectra in the resulting object should be ordered accordingly (first spectra from data origin "2" and then from "1"). Implementation of this method is optional since a default implementation for MsBackend is available.

• filterDataStorage(): filters the object retaining spectra matching the provided dataStorage. Parameter dataStorage has to be of type character and needs to match exactly the data storage value of the spectra to subset. filterDataStorage() should return the data ordered by the provided dataStorage parameter, i.e. if dataStorage = c("2", "1") was provided, the spectra in the resulting object should be ordered accordingly (first spectra from data storage "2" and then from "1"). Implementation of this method is optional since a default implementation for MsBackend is available.

• filterEmptySpectra(): removes empty spectra (i.e. spectra without peaks). Implementation of this method is optional since a default implementation for MsBackend is available.

• filterFile(): retains data of files matching the file index or file name provided with parameter file.

• filterIsolationWindow(): retains spectra that contain mz in their isolation window m/z range (i.e. with an isolationWindowLowerMz <= mz and isolationWindowUpperMz >= mz. Implementation of this method is optional since a default implementation for MsBackend is available.

• filterMsLevel(): retains spectra of MS level msLevel. Implementation of this method is optional since a default implementation for MsBackend is available.

• filterPolarity(): retains spectra of polarity polarity. Implementation of this method is optional since a default implementation for MsBackend is available.

• filterPrecursorMzRange() (previously filterPrecursorMz): retains spectra with a precursor m/z within the provided m/z range. Implementation of this method is optional since a default implementation for MsBackend is available.

• filterPrecursorMzValues(): retains spectra with a precursor m/z matching any of the provided m/z values (given ppm and tolerance). Implementation of this method is optional since a default implementation for MsBackend is available.

• filterPrecursorCharge(): retains spectra with the defined precursor charge(s). Implementation of this method is optional since a default implementation for MsBackend is available.

• filterPrecursorScan(): retains parent (e.g. MS1) and children scans (e.g. MS2) of acquisition number acquisitionNum. Parameter f is supposed to define the origin of the spectra (i.e. the original data file) to ensure related spectra from the same file/sample are selected and retained. Implementation of this method is optional since a default implementation for MsBackend is available.

• filterRanges(): allows filtering of the Spectra object based on user defined numeric ranges (parameter ranges) for one or more available spectra variables in object (spectra variable names can be specified with parameter spectraVariables). Spectra for which the value of a spectra variable is within it's defined range are retained. If multiple ranges/spectra variables are defined, the match parameter can be used to specify whether all conditions (match = "all"; the default) or if any of the conditions must match (match = "any"; all spectra for which values are within any of the provided ranges are retained). Implementation of this method is optional since a default implementation for MsBackend is available.

• filterRt(): retains spectra of MS level msLevel with retention times within (>=) rt[1] and (<=) rt[2]. Implementation of this method is optional since a default implementation for MsBackend is available.

• filterValues(): allows filtering of the Spectra object based on similarities of numeric values of one or more spectraVariables(object) (parameter spectraVariables) to provided values (parameter values) given acceptable differences (parameters tolerance and ppm). If multiple values/spectra variables are defined, the match parameter can be used to specify whether all conditions (match = "all"; the default) or if any of the conditions must match (match = "any"; all spectra for which values are within any of the provided ranges are retained). Implementation of this method is optional since a default implementation for MsBackend is available.

• intensity(): gets the intensity values from the spectra. Returns a IRanges::NumericList() of numeric vectors (intensity values for each spectrum). The length of the list is equal to the number of spectra in object.

• ⁠intensity<-⁠: replaces the intensity values. value has to be a list (or IRanges::NumericList()) of length equal to the number of spectra and the number of values within each list element identical to the number of peaks in each spectrum (i.e. the lengths(x)). Note that just writeable backends support this method.

• ionCount(): returns a numeric with the sum of intensities for each spectrum. If the spectrum is empty (see isEmpty()), NA_real_ is returned.

• isCentroided(): a heuristic approach assessing if the spectra in object are in profile or centroided mode. The function takes the qtl th quantile top peaks, then calculates the difference between adjacent m/z value and returns TRUE if the first quartile is greater than k. (See Spectra:::.peaks_is_centroided for the code.)

• isEmpty(): checks whether a spectrum in object is empty (i.e. does not contain any peaks). Returns a logical vector of length equal number of spectra.

• isolationWindowLowerMz(), ⁠isolationWindowLowerMz<-⁠: gets or sets the lower m/z boundary of the isolation window.

• isolationWindowTargetMz(), ⁠isolationWindowTargetMz<-⁠: gets or sets the target m/z of the isolation window.

• isolationWindowUpperMz(), ⁠isolationWindowUpperMz<-⁠: gets or sets the upper m/z boundary of the isolation window.

• isReadOnly(): returns a logical(1) whether the backend is read only or does allow also to write/update data.

• length(): returns the number of spectra in the object.

• lengths(): gets the number of peaks (m/z-intensity values) per spectrum. Returns an integer vector (length equal to the number of spectra). For empty spectra, 0 is returned.

• msLevel(): gets the spectra's MS level. Returns an integer vector (of length equal to the number of spectra) with the MS level for each spectrum (or NA_integer_ if not available).

• ⁠msLevel<-⁠: replaces the spectra's MS level.

• mz(): gets the mass-to-charge ratios (m/z) from the spectra. Returns a IRanges::NumericList() or length equal to the number of spectra, each element a numeric vector with the m/z values of one spectrum.

• ⁠mz<-⁠: replaces the m/z values. value has to be a list of length equal to the number of spectra and the number of values within each list element identical to the number of peaks in each spectrum (i.e. the lengths(x)). Note that just writeable backends support this method.

• polarity(), ⁠polarity<-⁠: gets or sets the polarity for each spectrum. polarity() returns an integer vector (length equal to the number of spectra), with 0 and 1 representing negative and positive polarities, respectively. ⁠polarity<-⁠ expects an integer vector of length 1 or equal to the number of spectra.

• precursorCharge(), precursorIntensity(), precursorMz(), precScanNum(), precAcquisitionNum(): get the charge (integer), intensity (numeric), m/z (numeric), scan index (integer) and acquisition number (interger) of the precursor for MS level 2 and above spectra from the object. Returns a vector of length equal to the number of spectra in object. NA are reported for MS1 spectra of if no precursor information is available.

• peaksData() returns a list with the spectras' peak data, i.e. m/z and intensity values or other peak variables. The length of the list is equal to the number of spectra in object. Each element of the list has to be a two-dimensional array (matrix or data.frame) with columns depending on the provided columns parameter (by default "mz" and "intensity", but depends on the backend's available peaksVariables). For an empty spectrum, a matrix (data.frame) with 0 rows and columns according to columns is returned. The optional parameter columns, if supported by the backend, allows to define which peak variables should be returned in the numeric peak matrix. As a default c("mz", "intensity") should be used.

• ⁠peaksData<-⁠ replaces the peak data (m/z 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 is 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.

• peaksVariables(): lists the available variables for mass peaks. Default peak variables are "mz" and "intensity" (which all backends need to support and provide), but some backends might provide additional variables. All these variables are expected to be returned (if requested) by the peaksData() function.

• reset() a backend (if supported). This method will be called on the backend by the ⁠reset,Spectra⁠ method that is supposed to restore the data to its original state (see ⁠reset,Spectra⁠ for more details). The function returns the reset backend. The default implementation for MsBackend returns the backend as-is.

• rtime(), ⁠rtime<-⁠: gets or sets the retention times for each spectrum (in seconds). rtime() returns a numeric vector (length equal to the number of spectra) with the retention time for each spectrum. ⁠rtime<-⁠ expects a numeric vector with length equal to the number of spectra.

• scanIndex(): returns an integer vector with the scan index for each spectrum. This represents the relative index of the spectrum within each file. Note that this can be different to the acquisitionNum() of the spectrum which is the index of the spectrum as reported in the mzML file.

• selectSpectraVariables(): reduces the information within the backend to the selected spectra variables. It is suggested to not remove values for the "dataStorage" variable, since this might be required for some backends to work properly (such as the MsBackendMzR).

• smoothed(),⁠smoothed<-⁠: gets or sets whether a spectrum is smoothed. smoothed() returns a logical vector of length equal to the number of spectra. ⁠smoothed<-⁠ takes a logical vector of length 1 or equal to the number of spectra in object.

• spectraData(), ⁠spectraData<-⁠: gets or sets general spectrum metadata (annotation, also called header). spectraData() returns a DataFrame, ⁠spectraData<-⁠ expects a DataFrame with the same number of rows as there are spectra in object. Note that spectraData() has to return the full data, i.e. also the m/z and intensity values (as a list or SimpleList in columns "mz" and "intensity".

• spectraNames(): returns a character vector with the names of the spectra in object or NULL if not set. ⁠spectraNames<-⁠ allows to set spectra names (if the object is not read-only).

• spectraVariables(): returns a character vector with the available spectra variables (columns, fields or attributes) available in object. This should return all spectra variables which are present in object, also "mz" and "intensity" (which are by default not returned by the ⁠spectraVariables,Spectra⁠ method).

• split(): splits the backend into a list of backends (depending on parameter f). The default method for MsBackend uses split.default(), thus backends extending MsBackend don't necessarily need to implement this method.

• supportsSetBackend(): whether a MsBackend supports the Spectra setBackend() function. For a MsBackend to support setBackend() it needs to have a parameter called data in its backendInitialize() method that support receiving all spectra data as a DataFrame from another backend and to initialize the backend with this data. In general read-only backends do not support setBackend() hence, the default implementation of supportsSetBackend() returns !isReadOnly(object). If a read-only backend would support the setBackend() and being initialized with a DataFrame an implementation of this method for that backend could be defined that returns TRUE (see also the MsBackend vignette for details and examples).

• tic(): gets the total ion current/count (sum of signal of a spectrum) for all spectra in object. By default, the value reported in the original raw data file is returned. For an empty spectrum, NA_real_ is returned.

• uniqueMsLevels(): gets the unique MS levels of all spectra in object. The default implementation calls unique(msLevel(object)) but more efficient implementations could be defined for specific backends.

Subsetting and merging backend classes

Backend classes must support (implement) the [ method to subset the object. This method should only support subsetting by spectra (rows, i) and has to return a MsBackend class.

Backends extending MsBackend should also implement the backendMerge() method to support combining backend instances (only backend classes of the same type should be merged). Merging should follow the following rules:

• The whole spectrum data of the various objects should be merged. The resulting merged object should contain the union of the individual objects' spectra variables (columns/fields), with eventually missing variables in one object being filled with NA.

In-memory data backends

MsBackendMemory and MsBackendDataFrame:

The MsBackendMemory and MsBackendDataFrame objects keep all MS data in memory are thus ideal for fast data processing. Due to their large memory footprint they are however not suited for large scale experiments. The two backends store the data different. The MsBackendDataFrame stores all data in a DataFrame and thus supports also S4-classes as spectra variables. Also, sepratate access to m/z or intensity values (i.e. using the mz() and intensity() methods) is faster for the MsBackendDataFrame. The MsBackendMemory on the other hand, due to the way the data is organized internally, provides much faster access to the full peak data (i.e. the numerical matrices of m/z and intensity values). Also subsetting and access to any spectra variable (except "mz" and "intensity") is fastest for the MsBackendMemory.

Thus, for most use cases, the MsBackendMemory provides a higher performance and flexibility than the MsBackendDataFrame and should thus be preferred. See also issue 246 for a performance comparison.

New objects can be created with the MsBackendMemory() and MsBackendDataFrame() function, respectively. Both backends can be subsequently initialized with the backendInitialize() method, taking a DataFrame (or data.frame) with the (full) MS data as first parameter data. The second parameter peaksVariables allows to define which columns in data contain peak variables such as the m/z and intensity values of individual peaks per spectrum. The default for this parameter is peaksVariables = c("mz", "intensity"). Note that it is not supported to provide either "mz" or "intensity", if provided, both need to be present in the data frame. Alternatively, the function also supports a data frame without m/z and intensity values, in which case a Spectra without mass peaks is created.

Suggested columns of this DataFrame are:

• "msLevel": integer with MS levels of the spectra.

• "rt": numeric with retention times of the spectra.

• "acquisitionNum": integer with the acquisition number of the spectrum.

• "scanIndex": integer with the index of the scan/spectrum within the mzML/mzXML/CDF file.

• "dataOrigin": character defining the data origin.

• "dataStorage": character indicating grouping of spectra in different e.g. input files. Note that missing values are not supported.

• "centroided": logical whether the spectrum is centroided.

• "smoothed": logical whether the spectrum was smoothed.

• "polarity": integer with the polarity information of the spectra.

• "precScanNum": integer specifying the index of the (MS1) spectrum containing the precursor of a (MS2) spectrum.

• "precursorMz": numeric with the m/z value of the precursor.

• "precursorIntensity": numeric with the intensity value of the precursor.

• "precursorCharge": integer with the charge of the precursor.

• "collisionEnergy": numeric with the collision energy.

• "mz": IRanges::NumericList() of numeric vectors representing the m/z values for each spectrum.

• "intensity": IRanges::NumericList() of numeric vectors representing the intensity values for each spectrum.

Additional columns are allowed too.

The peaksData() function for MsBackendMemory and MsBackendDataFrame returns a list of numeric matrix by default (with parameter columns = c("mz", "intensity")). If other peak variables are requested, a list of data.frame is returned (ensuring m/z and intensity values are always numeric).

MsBackendMzR, on-disk MS data backend

The MsBackendMzR keeps only a limited amount of data in memory, while the spectra data (m/z and intensity values) are fetched from the raw files on-demand. This backend uses the mzR package for data import and retrieval and hence requires that package to be installed. Also, it can only be used to import and represent data stored in mzML, mzXML and CDF files.

The MsBackendMzR backend extends the MsBackendDataFrame backend using its DataFrame to keep spectra variables (except m/z and intensity) in memory.

New objects can be created with the MsBackendMzR() function which can be subsequently filled with data by calling backendInitialize() passing the file names of the input data files with argument files.

This backend provides an export() method to export data from a Spectra in mzML or mzXML format. The definition of the function is:

export(object, x, file = tempfile(), format = c("mzML", "mzXML"), copy = FALSE)

The parameters are:

• object: an instance of the MsBackendMzR class.

• x: the Spectra object to be exported.

• file: character with the (full) output file name(s). Should be of length 1 or equal length(x). If a single file is specified, all spectra are exported to that file. Alternatively it is possible to specify for each spectrum in x the name of the file to which it should be exported (and hence file has to be of length equal length(x)).

• format: character(1), either "mzML" or "mzXML" defining the output file format.

• copy: logical(1) whether general file information should be copied from the original MS data files. This only works if x uses a MsBackendMzR backend and if dataOrigin(x) contains the original MS data file names.

• BPPARAM: parallel processing settings.

See examples in Spectra or the vignette for more details and examples.

The MsBackendMzR ignores parameter columns of the peaksData() function and returns always m/z and intensity values.

MsBackendHdf5Peaks, on-disk MS data backend

The MsBackendHdf5Peaks keeps, similar to the MsBackendMzR, peak data (i.e. m/z and intensity values) in custom data files (in HDF5 format) on disk while the remaining spectra variables are kept in memory. This backend supports updating and writing of manipulated peak data to the data files.

New objects can be created with the MsBackendHdf5Peaks() function which can be subsequently filled with data by calling the object's backendInitialize() method passing the desired file names of the HDF5 data files along with the spectra variables in form of a DataFrame (see MsBackendDataFrame for the expected format). An optional parameter hdf5path allows to specify the folder where the HDF5 data files should be stored to. If provided, this is added as the path to the submitted file names (parameter files).

By default backendInitialize() will store all peak data into a single HDF5 file which name has to be provided with the parameter files. To store peak data across several HDF5 files data has to contain a column "dataStorage" that defines the grouping of spectra/peaks into files: peaks for spectra with the same value in "dataStorage" are saved into the same HDF5 file. If parameter files is omitted, the value in dataStorage is used as file name (replacing any file ending with ".h5". To specify the file names, files' length has to match the number of unique elements in "dataStorage".

For details see examples on the Spectra() help page.

The MsBackendHdf5Peaks ignores parameter columns of the peaksData() function and returns always m/z and intensity values.

Author(s)

Johannes Rainer, Sebastian Gibb, Laurent Gatto, Philippine Louail

Examples

## The MsBackend class is a virtual class and can not be instantiated
## directly. Below we define a new backend class extending this virtual
## class
MsBackendDummy <- setClass("MsBackendDummy", contains = "MsBackend")
MsBackendDummy()

## This class inherits now all methods from `MsBackend`, all of which
## however throw an error. These methods would have to be implemented
## for the new backend class.
try(mz(MsBackendDummy()))

## See `MsBackendDataFrame` as a reference implementation for a backend
## class (in the *R/MsBackendDataFrame.R* file).

## MsBackendDataFrame
##
## The `MsBackendDataFrame` uses a `S4Vectors::DataFrame` to store all MS
## data. Below we create such a backend by passing a `DataFrame` with all
## data to it.
data <- DataFrame(msLevel = c(1L, 2L, 1L), scanIndex = 1:3)
data$mz <- list(c(1.1, 1.2, 1.3), c(1.4, 54.2, 56.4, 122.1), c(15.3, 23.2))
data$intensity <- list(c(3, 2, 3), c(45, 100, 12.2, 1), c(123, 12324.2))

## Backends are supposed to be created with their specific constructor
## function
be <- MsBackendDataFrame()

be

## The `backendInitialize()` method initializes the backend filling it with
## data. This method can take any parameters needed for the backend to
## get loaded with the data (e.g. a file name from which to load the data,
## a database connection or, in this case, a data frame containing the data).
be <- backendInitialize(be, data)

be

## Data can be accessed with the accessor methods
msLevel(be)

mz(be)

## Even if no data was provided for all spectra variables, its accessor
## methods are supposed to return a value.
precursorMz(be)

## The `peaksData()` method is supposed to return the peaks of the spectra as
## a `list`.
peaksData(be)

## List available peaks variables
peaksVariables(be)

## Use columns to extract specific peaks variables. Below we extract m/z and
## intensity values, but in reversed order to the default.
peaksData(be, columns = c("intensity", "mz"))

## List available spectra variables (i.e. spectrum metadata)
spectraVariables(be)

## Extract precursor m/z, rtime, MS level spectra variables
spectraData(be, c("precursorMz", "rtime", "msLevel"))

## MsBackendMemory
##
## The `MsBackendMemory` uses a more efficient internal data organization
## and allows also adding arbitrary additional peaks variables (annotations)
## Below we thus add a column "peak_ann" with arbitrary names/ids for each
## peak and add the name of this column to the `peaksVariables` parameter
## of the `backendInitialize()` method (in addition to `"mz"` and
## `"intensity"` that should **always** be specified.
data$peak_ann <- list(c("a", "", "d"), c("", "d", "e", "f"), c("h", "i"))
be <- backendInitialize(MsBackendMemory(), data,
    peaksVariables = c("mz", "intensity", "peak_ann"))
be

spectraVariables(be)

## peak_ann is also listed as a peaks variable
peaksVariables(be)

## The additional peaks variable can be accessed using the `peaksData()`
## function
peaksData(be, "peak_ann")

## The $<- method can be used to replace values of an existing peaks
## variable. It is important that the number of elements matches the
## number of peaks per spectrum.
be$peak_ann <- list(1:3, 1:4, 1:2)

## A peaks variable can again be removed by setting it to NULL
be$peak_ann <- NULL

peaksVariables(be)

rformassspectrometry/Spectra documentation built on Dec. 19, 2024, 1:05 p.m.