msc.rawMS.read.mzXML & msc.rawMS.write.mzXML {caMassClass} | R Documentation |
Read / write raw protein mass spectra to/from mzXML Files
msc.rawMS.write.mzXML(scans, filename, mzXML=NULL, ...) msc.rawMS.read.mzXML(input, scanIdx=NULL)
scans |
data to be stored in mzXML file, in form of a 2D matrix (nFeatures x nSamples) or 3D array (nFeatures x nSamples x nCopies). |
filename |
character string with name of the file (connection) |
mzXML |
class storing partially parsed mzXML data |
input |
Either mzXML object, or character string with name of the
file (connection) |
scanIdx |
List of scans to return. Optional. |
... |
additional parameters to be passed to write.mzXML
function |
Function read.mzXML
returns object of type
scans |
Data in the matrix format (nFeatures x nSamples)
rownames(scan) storing masses (M/Z) of each feature. |
mzXML |
Object of type mzXML . See read.mzXML for
details |
Functions msc.rawMS.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.peaks.read.mzXML
, msc.peaks.write.mzXML
functions also read/write mzXML file, but use different data format.
msc.rawMS.read.csv
function can read raw MS files from
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") # save raw MS data as mzXML msc.rawMS.write.mzXML(X, "rawMS32.mzXML", precision="32") Y = msc.rawMS.read.mzXML("rawMS32.mzXML") y = array(Y$scans, c(nrow(Y$scans), ncol(Y$scans)/2, 2)) stopifnot(all.equal(X,y, tolerance=1e-5)) # about the same msc.rawMS.write.mzXML(X, "rawMS64.mzXML", precision="64") Y = msc.rawMS.read.mzXML("rawMS64.mzXML") y = array(Y$scans, c(nrow(Y$scans), ncol(Y$scans)/2, 2)) stopifnot(X==y) # exactly the same # Suggestion: inspect 'rawMS32.mzXML' and 'rawMS64.mzXML' using a text editor file.remove("rawMS32.mzXML") # delete temporary files file.remove("rawMS64.mzXML")