MsBackendMapping: MS data backend for mapped text files

In meowcat/SpectraMapping: Mapping between spectra formats

MS data backend for mapped text files

Description

The MsBackendMapping class supports import of MS/MS spectra data from files in text format by a defined mapping. After initial import, the full MS data is kept in memory. MsBackendMapping uses tibble/tidyverse stuff in the background.

New objects are created with the MsBackendMapping function. The backendInitialize method has to be subsequently called to initialize the object and import MS/MS data from (one or more) files. Optional parameter nonStop allows to specify whether the import returns with an error if one of the xml files lacks required data, such as mz and intensity values (default nonStop = FALSE), or whether only affected file(s) is(are) skipped and a warning is shown (nonStop = TRUE). Note that any other error (such as xml import error) will abort import regardless of parameter nonStop.

Usage

## S4 method for signature 'MsBackendMapping'
backendInitialize(object, files, data, nonStop = FALSE, parallel = FALSE, ...)

MsBackendMapping(format, fields = .load_default_fields())

Arguments

object	Instance of MsBackendMapping class.
files	character with the (full) file name(s) of the file(s) from which MS/MS data should be imported.
nonStop	logical(1) whether import should be stopped if an xml file does not contain all required fields. Defaults to nonStop = FALSE.
...	Currently ignored.
BPPARAM	Parameter object defining the parallel processing setup to import data in parallel. Defaults to BPPARAM = bpparam(). See bpparam() for more information.

Author(s)

Michele Stravs [e-mail]

meowcat/SpectraMapping documentation built on May 14, 2024, 6:30 p.m.