R/readMSData.R
readMSData.Rd
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")
)
A character
with file names to be read and parsed.
An object of class AnnotatedDataFrame or
NULL
(default).
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.
Verbosity flag. Default is to use
isMSnbaseVerbose()
.
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.
A logical
indicating whether spectra already
smoothed or not. Default is NA
.
Numeric indicating caching level. Default is 0 for
MS1 and 1 MS2 (or higher). Only relevant for inMemory
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.
An MSnExp object for inMemory
mode and a
OnDiskMSnExp object for onDisk
mode.
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.
readMSData
uses normalizePath
to replace relative with
absolute file paths.
readMgfData()
to read mgf
peak lists.
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: Mon Nov 6 08:25:26 2023
#> MSnbase version: 2.29.1
#> - - - 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 [Mon Nov 6 08:25:27 2023]
#> MSnbase version: 2.29.1
#> - - - 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)'