msc.peaks.read.mzXML & msc.peaks.write.mzXML {caMassClass} | R Documentation |
Functions to read and write mzXML files containing peaks stored in the format used by peak finding functions.
msc.peaks.write.mzXML(scans, filename, mzXML=NULL, ...) msc.peaks.read.mzXML(filename)
scans |
Peak information to be stored in mzXML file. A data-frame in the
similar to format as returned by msc.peaks.find , containing
four components:
|
filename |
character string with name of the file. |
mzXML |
class storing partially parsed mzXML data |
... |
additional parameters to be passed to write.mzXML
function (precision) |
Functions read.mzXML
and write.mzXML
use very
general data type to comunicate with mzXML
files. Functions
msc.rawMS.read.mzXML
and msc.rawMS.write.mzXML
allow passing informations using data format specialized for storing
peak data.
Function msc.peaks.read.mzXML
returns list with folowing objects:
scans |
Data in the same format as msc.peaks.write.mzXML input
parameter scans . |
mzXML |
Object of type mzXML . See read.mzXML for
details |
Functions msc.peaks.write.mzXML
do not return anything.
Jarek Tuszynski (SAIC) jaroslaw.w.tuszynski@saic.com
read.mzXML
, write.mzXML
are more genaral
mzXML file reader/writer.
msc.rawMS.read.mzXML
& msc.rawMS.write.mzXML
functions also read/write mzXML file, but use different data format.
msc.peaks.read.csv
& msc.peaks.write.mzXML
function can read/write peak data using CSV files.
# load "Data_IMAC.Rdata" file containing raw MS spectra 'X' if (!file.exists("Data_IMAC.Rdata")) example("msc.project.read") load("Data_IMAC.Rdata") # Find Peaks and save them Peaks = msc.peaks.find(X) # create peak data msc.peaks.write.mzXML(Peaks, "peaks.mzXML", precision='64') X = msc.peaks.read.mzXML("peaks.mzXML") stopifnot(X$scans$Substance.Mass == Peaks$Substance.Mass, X$scans$Intensity == Peaks$Intensity, X$scans$Spectrum.==Peaks$Spectrum., X$scans$Peak.==Peaks$Peak.) # Suggestion: inspect 'peaks.mzXML' using any text editor file.remove("peaks.mzXML")