Description Usage Arguments Author(s) See Also Examples
Accessors to the analytical setup metadata of a run.
runInfo
will show a summary of the experiment as a named list,
including scanCount
, lowMZ
, highMZ
,
dStartTime
, dEndTime
and startTimeStamp
. Note
that startTimeStamp
can only be extracted from mzML
files using the pwiz backend or from CDF files. A
NA
is reported if its value is not available.
The instrumentInfo
method returns a named list
including
instrument manufacturer, model, ionisation technique, analyzer and
detector. mzRpwiz
will give more additional information including
information on sample, software using and original source file.
These individual pieces of information can also be directly
accessed by the specific methods.
mzidInfo
is used for the mzR
object created from a mzid file.
It returns basic information on this mzid file including file provider,
creation date, software, database, enzymes and spectra data format.
The mzidInfo
will return the scoring results in identification.
It will return different results for different searching software used.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | runInfo(object)
chromatogramsInfo(object)
analyzer(object)
detector(object)
instrumentInfo(object)
ionisation(object)
softwareInfo(object)
sampleInfo(object)
sourceInfo(object)
model(object)
mzidInfo(object)
modifications(object, ...)
psms(object, ...)
substitutions(object)
database(object, ...)
enzymes(object)
tolerance(object, ...)
score(x, ...)
para(object)
specParams(object)
|
object |
An instantiated |
x |
An instantiated |
... |
Additional arguments, currently ignored. |
Steffen Neumann, Laurent Gatto and Qiang Kou
See for example peaks
to access the data for the spectra
in a "mzR"
class.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | library(msdata)
file <- system.file("microtofq/MM8.mzML", package = "msdata")
mz <- openMSfile(file)
fileName(mz)
instrumentInfo(mz)
runInfo(mz)
close(mz)
file <- system.file("cdf/ko15.CDF", package = "msdata")
mz <- openMSfile(file, backend = "netCDF")
fileName(mz)
instrumentInfo(mz)
runInfo(mz)
close(mz)
file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")
mzid <- openIDfile(file)
softwareInfo(mzid)
enzymes(mzid)
|
Loading required package: Rcpp
[1] "/usr/lib/R/site-library/msdata/microtofq/MM8.mzML"
$manufacturer
[1] "Bruker Daltonics micrOTOF series"
$model
[1] "micrOTOF-Q"
$ionisation
[1] "electrospray ionization"
$analyzer
[1] "quadrupole"
$detector
[1] "electron multiplier"
$software
[1] "exportSoftware 3.0.0"
$sample
[1] "MM8sample"
$source
[1] ""
$scanCount
[1] 198
$lowMz
[1] 95.51765
$highMz
[1] 1005.043
$dStartTime
[1] 0.486
$dEndTime
[1] 66.7818
$msLevels
[1] 1
$startTimeStamp
[1] "2008-09-01T09:48:37.296+01:00"
[1] "/usr/lib/R/site-library/msdata/cdf/ko15.CDF"
$model
[1] " "
$manufacturer
[1] "Agilent Technologies"
$ionisation
[1] "Electrospray Ionization"
$detector
[1] "Conversion Dynode Electron Multiplier"
$analyzer
[1] NA
$scanCount
[1] 1278
$lowMz
[1] 200
$highMz
[1] 600
$dStartTime
[1] 2501.378
$dEndTime
[1] 4499.824
$msLevels
[1] NA
$startTimeStamp
[1] "2004,06,01,10:28:03+0800"
[1] "xtandem x! tandem CYCLONE (2010.06.01.5) "
[2] "ProteoWizard MzIdentML 3.0.501 ProteoWizard"
name nTermGain cTermGain minDistance missedCleavages
1 Trypsin H OH 0 1
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