| 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, wipe=TRUE)
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. By default all will be returned, but one can choose only a subset using this argument. |
wipe |
Should all scans that were returned be also deleted (wiped) from
mzXML record? Set to TRUE by default to minimize memory use. |
... |
additional parameters to be passed to write.mzXML
function |
Function msc.rawMS.read.mzXML returns data in the matrix format (nFeatures
x nSamples) rownames(scan) storing masses (M/Z)
of each feature. In addition, object of type mzXML is attached
as "mzXML" attribute. 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 general
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 using 32-bit precision
msc.rawMS.write.mzXML(X, "rawMS32.mzXML", precision="32")
Y = msc.rawMS.read.mzXML("rawMS32.mzXML")
dim(Y) = c(nrow(Y), ncol(Y)/2, 2)
stopifnot(all.equal(X,Y, tolerance=1e-5, check.attributes = FALSE)) # about the same
# save raw MS data as mzXML using 64-bit precision
msc.rawMS.write.mzXML(X, "rawMS64.mzXML", precision="64")
Y = msc.rawMS.read.mzXML("rawMS64.mzXML")
dim(Y) = c(nrow(Y), ncol(Y)/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")