MsBackendCompDb: CompDb-based MS spectrum backend

In michaelwitting/CompoundDb: Creating and using (Chemical) Compound Annotation Databases

Description

The MsBackendCompDb allows to retrieve MS2 spectra from an CompDb() object/database. The object keeps only a limited amount of data in memory and retrieves the m/z and intensity values from the database on-demand.

It is not intended that users create or use instances of this class directly, the Spectra() call on CompDb() will return a Spectra object that uses this backend.

Usage

MsBackendCompDb()

## S4 method for signature 'MsBackendCompDb'
backendInitialize(object, x, columns, filter, ...)

## S4 method for signature 'MsBackendCompDb'
show(object)

## S4 method for signature 'MsBackendCompDb'
as.list(x)

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

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

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

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

## S4 method for signature 'MsBackendCompDb'
asDataFrame(object, columns = spectraVariables(object))

## S4 replacement method for signature 'MsBackendCompDb'
asDataFrame(object) <- value

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

Arguments

object	an MsBackendCompDb instance.
x	an MsBackendCompDb instance.
columns	for asDataFrame: character with names of columns/spectra variables that should be returned. Defaults to spectraVariables(object).
filter	for backendInitialize: optional filter expression to specify which elements to retrieve from the database.
...	ignored.
value	for $<-: the replacement values.
name	for $<-: the name of the spectra variable to replace.

Methods implemented for MsBackendCompDb

The methods listed here are implemented for the MsBackendCompDb. All other methods are inherited directly from the parent MsBackendDataFrame() class. See that help page for a complete listing of methods.

• as.list: gets the full list of peak matrices. Returns a SimpleList(), length equal to the number of spectra and each element being a matrix with columns "mz" and "intensity" with the spectra's m/z and intensity values.

• intensity: retrieves the intensity values for all spectra. Returns a NumericList(), each element being the intensity values of one spectrum. The actual intensity values are retrieved from the database.

• intensity<-: not supported.

• mz: retrieves the m/z values for all spectra. Returns a NumericList(), each element being a numeric with the m/z values of one spectrum. These values are retrieved from the database.

• mz<-: not supported.

• asDataFrame: returns the complete spectrum data including m/z and intensity values as a DataFrame().

• asDataFrame<-: replace the spectrum metadata. Note that columns "mz" and "intensity" are ignored.

• $<-: replace or add a spectrum variable. Note that mz, intensity and spectrum_id variables can not be replaced.

Note

For higher performance it is suggested to change the backend of the Spectra() object to an MsBackendDataFrame() backend with the setBackend() method of Spectra objects.

Author(s)

Johannes Rainer

michaelwitting/CompoundDb documentation built on April 29, 2020, 8:42 p.m.