Description Usage Arguments Author(s) Examples
The openMSfile
constructor will create a new format-specifc
mzR
object, open 'filename' file and all header information is
loaded as a Rcpp module and made accessible through the ramp
or pwiz
slot of the resulting object.
The openIDfile
constructor will create a new format-specifc
mzR
object, open 'filename' file and all information is
loaded as a Rcpp module. The mzid format is supported throught
pwiz
backend. Only mzIdentML 1.1 is supported.
1 2 3 4 5 6 7 8 9 | openMSfile(filename, backend = NULL, verbose = FALSE)
initializeRamp(object)
isInitialized(object)
fileName(object, ...)
openIDfile(filename, verbose = FALSE)
|
filename |
Path name of the netCDF, mzData, mzXML or mzML file to read/write. |
backend |
A |
object |
An instantiated mzR object. |
verbose |
Enable verbose output. |
... |
Additional arguments, currently ignored. |
Steffen Neumann, Laurent Gatto, Qiang Kou
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | library(msdata)
filepath <- system.file("microtofq", package = "msdata")
file <- list.files(filepath, pattern="MM14.mzML",
full.names=TRUE, recursive = TRUE)
mz <- openMSfile(file)
fileName(mz)
runInfo(mz)
close(mz)
## Not run:
## to use another backend
mz <- openMSfile(file, backend = "pwiz")
mz
## End(Not run)
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/MM14.mzML"
$scanCount
[1] 112
$lowMz
[1] 0
$highMz
[1] 0
$dStartTime
[1] 270.334
$dEndTime
[1] 307.678
$msLevels
[1] 1
$startTimeStamp
[1] NA
Mass Spectrometry file handle.
Filename: MM14.mzML
Number of scans: 112
[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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