readMSData {MSnbase} | R Documentation

## 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

### See Also

`readMgfData()` to read `mgf` peak lists.

### 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

[Package MSnbase version 2.20.1 Index]