MSnbase: readMSData – R documentation

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readMSData

Imports mass-spectrometry raw data files as 'MSnExp' instances.

Description

Reads as set of XML-based mass-spectrometry data files and generates an MSnExp object. This function uses the functionality provided by the mzR package to access data and meta data in mzData, mzXML and mzML.

Usage

readMSData(
  files,
  pdata = NULL,
  msLevel. = NULL,
  verbose = isMSnbaseVerbose(),
  centroided. = NA,
  smoothed. = NA,
  cache. = 1L,
  mode = c("inMemory", "onDisk")
)

Arguments

`files`	A `character` with file names to be read and parsed.
`pdata`	An object of class AnnotatedDataFrame or `NULL` (default).
`msLevel.`	MS level spectra to be read. In `inMemory` mode, use `1` for MS1 spectra or any larger numeric for MSn spectra. Default is `2` for `InMemory` mode. `onDisk` mode supports multiple levels and will, by default, read all the data.
`verbose`	Verbosity flag. Default is to use `isMSnbaseVerbose()`.
`centroided.`	A `logical`, indicating whether spectra are centroided or not. Default is `NA` in which case the information is extracted from the raw file (for mzML or mzXML files). In `onDisk`, it can also be set for different MS levels by a vector of logicals, where the first element is for MS1, the second element is for MS2, ... See OnDiskMSnExp for an example.
`smoothed.`	A `logical` indicating whether spectra already smoothed or not. Default is `NA`.
`cache.`	Numeric indicating caching level. Default is 0 for MS1 and 1 MS2 (or higher). Only relevant for `inMemory` mode.
`mode`	On of `"inMemory"` (default) or `"onDisk"`. The former loads the raw data in memory, while the latter only generates the object and the raw data is accessed on disk when needed. See the benchmarking vignette for memory and speed implications.

Details

When using the inMemory mode, the whole MS data is read from file and kept in memory as Spectrum objects within the MSnExp'es assayData slot.

To reduce the memory footpring especially for large MS1 data sets it is also possible to read only selected information from the MS files and fetch the actual spectrum data (i.e. the M/Z and intensity values) only on demand from the original data files. This can be achieved by setting mode = "onDisk". The function returns then an OnDiskMSnExp object instead of a MSnExp object.

Value

An MSnExp object for inMemory mode and a OnDiskMSnExp object for onDisk mode.

Note

readMSData uses normalizePath to replace relative with absolute file paths.

Author(s)

Laurent Gatto

Examples

file <- dir(system.file(package = "MSnbase", dir = "extdata"),
            full.name = TRUE,
            pattern = "mzXML$")
mem <- readMSData(file, mode = "inMemory")
mem
dsk <- readMSData(file, mode = "onDisk")
dsk

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release