mzR
object.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.
header(object, scans, ...) peaksCount(object, scans, ...)
peaks(object, ...)
get3Dmap(object, scans, lowMz, highMz, resMz, ...)
mzR
object.numeric
specifying which scans to
return. Optional for the header
, peaks
and
peaksCount
methods. If ommited, the requested data for all
peaks is returned.Numeric
s defining the m/z range to be returned.numeric
defining the m/z resolution.scan
parameter can be passed to
peaks
.instrumentInfo
for metadata access and the
"mzR "
class.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)