peaks: Access the raw data from an 'mzR' object.

In sneumann/mzR-playground: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

Description

Access the MS raw data. The peaks and peaksCount functions return the (m/z,intensity) pairs and the number peaks in the spectrum/spectra. peaks returns a single matrix if scans is a numeric of length 1 and a list of matrices if several scans are asked for or no scans argument is provided (i.e all spectra in the oject are retured). peaksCount will return a numeric of length n.

The header function returns a list containing seqNum, acquisitionNum , msLevel, peaksCount, totIonCurrent, retentionTime, basePeakMZ, basePeakIntensity, collisionEnergy, ionisationEnergy, lowM, highMZ, precursorScanNum, precursorMZ, precursorCharge, precursorIntensity, mergedScan, mergedResultScanNum, mergedResultStartScanNum and mergedResultEndScanNum, when available in the original file. If multiple scans are queried, a data.frame is returned with the scans reported along the rows.

The get3Dmap function performs a simple resampling between lowMz and highMz with reMz resolution. A matrix of dimensions length(scans) times seq(lowMz,highMz,resMz) is returned.

Usage

 header(object, scans, ...)

 peaksCount(object, scans, ...)

 peaks(object, scans, ...)

 get3Dmap(object, scans, lowMz, highMz, resMz, ...)

Arguments

object	An instantiated mzR object.
scans	A numeric specifying which scans to return. Optional for the header, peaks and peaksCount methods. If ommited, the requested data for all peaks is returned.
lowMz, highMz	Numerics defining the m/z range to be returned.
resMz	a numeric defining the m/z resolution.
...	Other arguments. Currently ignored.

Author(s)

Steffen Neumann and Laurent Gatto

See Also

instrumentInfo for metadata access and the "mzR" class.

Examples

 library(msdata)
 filepath <- system.file("microtofq", package = "msdata")
 file <- list.files(filepath, pattern="MM14.mzML",
                    full.names=TRUE, recursive = TRUE)
  mz <- openMSfile(file)
  runInfo(mz)
  colnames(header(mz))
  close(mz)

sneumann/mzR-playground documentation built on May 30, 2019, 6 a.m.