Chromatographic Data Backend for Reading mzML Files — ChromBackendMzR • Chromatograms

The ChromBackendMzR inherits all slots and methods from the base ChromBackendMemory backend, providing additional functionality for reading chromatographic data from mzML files.

Unlike the ChromBackendMemory backend, the ChromBackendMzR backend should have the dataOrigin chromatographic variables populated with the file path of the mzML file from which the chromatographic data was read.

Note that the ChromBackendMzR backend is read-only and does not support direct modification of chromatographic data. However, it does support peaksData slot replacement, which will modify the @peaksData slot but not the local mzML files. This is indicated by the "inMemory" slot being set to TRUE.

Implementing functionalities with the ChromBackendMzR backend should be simplified as much as possible and reuse the methods already implemented for ChromBackendMemory when possible.

Usage

ChromBackendMzR()

# S4 method for class 'ChromBackendMzR'
backendInitialize(object, files = character(), BPPARAM = bpparam(), ...)

Arguments

object: A ChromBackendMzR object.
files: A character vector of file paths to mzML files.
BPPARAM: Parallel setup configuration. See BiocParallel::bpparam() for more information.
...: Additional parameters to be passed.

Value

Refer to the individual function description for information on the return value.

Author

Philippine Louail

Examples

library(mzR)
#> Loading required package: Rcpp
library(MsDataHub)

## Load an mzML file
MRM_file <- MRM.standmix.5.mzML()
#> see ?MsDataHub and browseVignettes('MsDataHub') for documentation
#> loading from cache

## Initialize the ChromBackendMzR object
be_empty <- ChromBackendMzR()
be <- backendInitialize(be_empty, files = MRM_file, BPPARAM = SerialParam())