Conversion between objects from the Spectra and MSnbase packages
Source:R/functions-MSpectra.R
extractSpectraData.RdThe Spectra package provides a more robust and efficient infrastructure for mass spectrometry data handling and analysis. So, wherever possible, the newer Spectra package should be used instead of the MSnbase. The functions listed here allow to convert between objects from the MSnbase and Spectra packages.
extractSpectraData extracts the spectra data (m/z and intensity values
including metadata) from MSnExp, OnDiskMSnExp,
Spectrum1, Spectrum2 objects (or list of such objects) and
returns these as a DataFrame that can be used to create a
Spectra::Spectra object.This function enables thus
to convert data from the old MSnbase package to the newer Spectra
package.
To convert a Spectra object to a MSpectra object use
as(sps, "MSpectra") where sps is a Spectra object.
Value
extracSpectraData()returns aDataFrame()with the full spectrum data that can be passed to theSpectra::Spectra()function to create aSpectraobject.as(x, "MSpectra")returns aMSpectraobject with the content of theSpectraobjectx.
Note
Coercion from Spectra to a MSpectra will only assign values to the
contained Spectrum1 and Spectrum2 objects, but will not add all
eventually spectra variables present in Spectra.
Examples
## Read an mzML file with MSnbase
fl <- system.file("TripleTOF-SWATH", "PestMix1_SWATH.mzML",
package = "msdata")
data <- filterRt(readMSData(fl, mode = "onDisk"), rt = c(1, 6))
## Extract the data as a DataFrame
res <- extractSpectraData(data)
res
#> DataFrame with 50 rows and 38 columns
#> fromFile spIdx smoothed scanIndex acquisitionNum msLevel
#> <integer> <integer> <logical> <integer> <integer> <integer>
#> F1.S0010 1 10 NA 10 10 2
#> F1.S0011 1 11 NA 11 11 2
#> F1.S0012 1 12 NA 12 12 2
#> F1.S0013 1 13 NA 13 13 2
#> F1.S0014 1 14 NA 14 14 2
#> ... ... ... ... ... ... ...
#> F1.S0055 1 55 NA 55 55 2
#> F1.S0056 1 56 NA 56 56 2
#> F1.S0057 1 57 NA 57 57 2
#> F1.S0058 1 58 NA 58 58 2
#> F1.S0059 1 59 NA 59 59 2
#> polarity originalPeaksCount totIonCurrent rtime basePeakMZ
#> <integer> <integer> <numeric> <numeric> <numeric>
#> F1.S0010 1 340 83853 1.101 141.946
#> F1.S0011 1 491 61072 1.198 217.106
#> F1.S0012 1 296 28639 1.295 217.108
#> F1.S0013 1 301 26285 1.392 149.024
#> F1.S0014 1 292 27660 1.489 281.049
#> ... ... ... ... ... ...
#> F1.S0055 1 373 89856 5.601 141.946
#> F1.S0056 1 532 66566 5.698 217.108
#> F1.S0057 1 301 30835 5.795 217.106
#> F1.S0058 1 256 23034 5.892 279.098
#> F1.S0059 1 310 27343 5.989 281.051
#> basePeakIntensity collisionEnergy ionisationEnergy lowMZ highMZ
#> <numeric> <numeric> <numeric> <numeric> <numeric>
#> F1.S0010 6580 0 0 0 0
#> F1.S0011 1429 0 0 0 0
#> F1.S0012 501 0 0 0 0
#> F1.S0013 413 0 0 0 0
#> F1.S0014 714 0 0 0 0
#> ... ... ... ... ... ...
#> F1.S0055 7477 0 0 0 0
#> F1.S0056 1400 0 0 0 0
#> F1.S0057 432 0 0 0 0
#> F1.S0058 186 0 0 0 0
#> F1.S0059 496 0 0 0 0
#> precursorScanNum precursorMZ precursorCharge precursorIntensity
#> <integer> <numeric> <integer> <numeric>
#> F1.S0010 NA 163.75 0 0
#> F1.S0011 NA 208.95 0 0
#> F1.S0012 NA 244.05 0 0
#> F1.S0013 NA 270.85 0 0
#> F1.S0014 NA 299.10 0 0
#> ... ... ... ... ...
#> F1.S0055 NA 163.75 0 0
#> F1.S0056 NA 208.95 0 0
#> F1.S0057 NA 244.05 0 0
#> F1.S0058 NA 270.85 0 0
#> F1.S0059 NA 299.10 0 0
#> mergedScan mergedResultScanNum mergedResultStartScanNum
#> <integer> <integer> <integer>
#> F1.S0010 NA NA NA
#> F1.S0011 NA NA NA
#> F1.S0012 NA NA NA
#> F1.S0013 NA NA NA
#> F1.S0014 NA NA NA
#> ... ... ... ...
#> F1.S0055 NA NA NA
#> F1.S0056 NA NA NA
#> F1.S0057 NA NA NA
#> F1.S0058 NA NA NA
#> F1.S0059 NA NA NA
#> mergedResultEndScanNum injectionTime filterString spectrumId
#> <integer> <numeric> <character> <character>
#> F1.S0010 NA 0 NA sample=1 p...
#> F1.S0011 NA 0 NA sample=1 p...
#> F1.S0012 NA 0 NA sample=1 p...
#> F1.S0013 NA 0 NA sample=1 p...
#> F1.S0014 NA 0 NA sample=1 p...
#> ... ... ... ... ...
#> F1.S0055 NA 0 NA sample=1 p...
#> F1.S0056 NA 0 NA sample=1 p...
#> F1.S0057 NA 0 NA sample=1 p...
#> F1.S0058 NA 0 NA sample=1 p...
#> F1.S0059 NA 0 NA sample=1 p...
#> centroided ionMobilityDriftTime isolationWindowTargetMZ
#> <logical> <numeric> <numeric>
#> F1.S0010 TRUE NA 163.75
#> F1.S0011 TRUE NA 208.95
#> F1.S0012 TRUE NA 244.05
#> F1.S0013 TRUE NA 270.85
#> F1.S0014 TRUE NA 299.10
#> ... ... ... ...
#> F1.S0055 TRUE NA 163.75
#> F1.S0056 TRUE NA 208.95
#> F1.S0057 TRUE NA 244.05
#> F1.S0058 TRUE NA 270.85
#> F1.S0059 TRUE NA 299.10
#> isolationWindowLowerOffset isolationWindowUpperOffset
#> <numeric> <numeric>
#> F1.S0010 24.25 24.25
#> F1.S0011 21.95 21.95
#> F1.S0012 14.15 14.15
#> F1.S0013 13.65 13.65
#> F1.S0014 15.60 15.60
#> ... ... ...
#> F1.S0055 24.25 24.25
#> F1.S0056 21.95 21.95
#> F1.S0057 14.15 14.15
#> F1.S0058 13.65 13.65
#> F1.S0059 15.60 15.60
#> scanWindowLowerLimit scanWindowUpperLimit electronBeamEnergy spectrum
#> <numeric> <numeric> <numeric> <integer>
#> F1.S0010 140 900 NA 10
#> F1.S0011 140 900 NA 11
#> F1.S0012 140 900 NA 12
#> F1.S0013 140 900 NA 13
#> F1.S0014 140 900 NA 14
#> ... ... ... ... ...
#> F1.S0055 140 900 NA 55
#> F1.S0056 140 900 NA 56
#> F1.S0057 140 900 NA 57
#> F1.S0058 140 900 NA 58
#> F1.S0059 140 900 NA 59
#> mz intensity
#> <NumericList> <NumericList>
#> F1.S0010 140.888,140.949,140.974,... 0.0999316,2.6204529,0.5139834,...
#> F1.S0011 140.901,140.913,140.958,... 0.0999386,0.1832319,0.5464582,...
#> F1.S0012 140.992,141.090,141.104,... 0.0599841,0.2358523,0.0800102,...
#> F1.S0013 140.872,141.957,143.089,... 0.0199862,0.0200630,0.0604285,...
#> F1.S0014 140.872,140.960,141.970,... 0.0799445,0.0199924,0.0200639,...
#> ... ... ...
#> F1.S0055 140.949,140.967,140.983,... 1.384358,0.183261,0.337385,...
#> F1.S0056 140.045,140.912,140.955,... 0.0597824,0.1823982,0.2357384,...
#> F1.S0057 141.094,141.963,141.981,... 0.288360,0.120379,0.100323,...
#> F1.S0058 140.876,141.955,141.972,... 0.0999327,0.1237221,0.0200640,...
#> F1.S0059 141.098,141.957,141.972,... 0.180017,0.020063,0.140449,...
library(Spectra)
#>
#> Attaching package: ‘Spectra’
#> The following objects are masked from ‘package:MSnbase’:
#>
#> combineSpectra, pickPeaks, plotMzDelta
## This can be used as an input for the Spectra constructor of the
## Spectra package:
sps <- Spectra::Spectra(res)
sps
#> MSn data (Spectra) with 50 spectra in a MsBackendMemory backend:
#> msLevel rtime scanIndex
#> <integer> <numeric> <integer>
#> F1.S0010 2 1.101 10
#> F1.S0011 2 1.198 11
#> F1.S0012 2 1.295 12
#> F1.S0013 2 1.392 13
#> F1.S0014 2 1.489 14
#> ... ... ... ...
#> F1.S0055 2 5.601 55
#> F1.S0056 2 5.698 56
#> F1.S0057 2 5.795 57
#> F1.S0058 2 5.892 58
#> F1.S0059 2 5.989 59
#> ... 42 more variables/columns.
## A Spectra object can be coerced to a MSnbase MSpectra object using
msps <- as(sps, "MSpectra")