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.

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.

Value

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

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.

Note

readMSData uses normalizePath to replace relative with absolute file paths.

See also

readMgfData() to read mgf peak lists.

Author

Laurent Gatto

Examples

file <- dir(system.file(package = "MSnbase", dir = "extdata"),
            full.name = TRUE,
            pattern = "mzXML$")
mem <- readMSData(file, mode = "inMemory")
mem
#> MSn experiment data ("MSnExp")
#> Object size in memory: 0.18 Mb
#> - - - Spectra data - - -
#>  MS level(s): 2 
#>  Number of spectra: 5 
#>  MSn retention times: 25:01 - 25:02 minutes
#> - - - Processing information - - -
#> Data loaded: Thu Sep  9 06:10:51 2021 
#>  MSnbase version: 2.19.3 
#> - - - Meta data  - - -
#> phenoData
#>   rowNames: dummyiTRAQ.mzXML
#>   varLabels: sampleNames
#>   varMetadata: labelDescription
#> Loaded from:
#>   dummyiTRAQ.mzXML 
#> protocolData: none
#> featureData
#>   featureNames: F1.S1 F1.S2 ... F1.S5 (5 total)
#>   fvarLabels: spectrum
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
dsk <- readMSData(file, mode = "onDisk")
dsk
#> MSn experiment data ("OnDiskMSnExp")
#> Object size in memory: 0.03 Mb
#> - - - Spectra data - - -
#>  MS level(s): 2 
#>  Number of spectra: 5 
#>  MSn retention times: 25:01 - 25:02 minutes
#> - - - Processing information - - -
#> Data loaded [Thu Sep  9 06:10:52 2021] 
#>  MSnbase version: 2.19.3 
#> - - - Meta data  - - -
#> phenoData
#>   rowNames: dummyiTRAQ.mzXML
#>   varLabels: sampleNames
#>   varMetadata: labelDescription
#> Loaded from:
#>   dummyiTRAQ.mzXML 
#> protocolData: none
#> featureData
#>   featureNames: F1.S1 F1.S2 ... F1.S5 (5 total)
#>   fvarLabels: fileIdx spIdx ... spectrum (35 total)
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'