writeMSData {mzR} | R Documentation |
Write MS spectrum data to an MS file
Description
writeMSData
exports the MS spectrum data provided with
parameters header
and data
to an MS file in mzML or
mzXML format.
Usage
## S4 method for signature 'list,character'
writeMSData(object, file, header,
backend = "pwiz", outformat = "mzml", rtime_seconds = TRUE,
software_processing)
Arguments
object |
list containing for each spectrum one matrix with
columns mz (first column) and intensity (second
column). See also peaks for the method that reads such
data from an MS file.
|
file |
character(1) defining the name of the file.
|
header |
data.frame with the header data for the spectra. Has to be in
the format as the data.frame returned by the
header method.
|
backend |
character(1) defining the backend that should be used for
writing. Currently only "pwiz" backend is supported.
|
outformat |
character(1) the format of the output file. One of
"mzml" or "mzxml" .
|
rtime_seconds |
logical(1) whether the retention time is provided in seconds
or minutes (defaults to TRUE ).
|
software_processing |
list of character vectors (or single character
vector). Each character vector providing information about
the software that was used to process the data with optional
additional description of processing steps. The length of each
character vector has to be >= 3: the first element being the
name of the software, the second string its version and the third
element the MS CV ID of the software (or "MS:-1" if not
known). All additional elements are optional and represent the MS CV
ID of each processing step performed with the software.
|
Author(s)
Johannes Rainer
See Also
copyWriteMSData
for a function to copy general
information from a MS data file and writing eventually modified MS
data from that originating file.
Examples
## Open a MS file and read the spectrum and header information
library(msdata)
fl <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML",
package = "msdata")
ms_fl <- openMSfile(fl, backend = "pwiz")
## Get the spectra
pks <- spectra(ms_fl)
## Get the header
hdr <- header(ms_fl)
## Modify the spectrum data adding 100 to each intensity.
pks <- lapply(pks, function(z) {
z[, 2] <- z[, 2] + 100
z
})
## Write the data to a mzML file.
out_file <- tempfile()
writeMSData(object = pks, file = out_file, header = hdr)
[Package
mzR version 2.18.1
Index]