copyWriteMSData: Write MS spectrum data to a MS file copying metadata from the...

In sneumann/mzR: parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)

Write MS spectrum data to a MS file copying metadata from the originating file

Description

Copy general information from the originating MS file and write this, along with the provided spectra data, to a new file. The expected workflow is the following: data is first loaded from an MS file, e.g. using peaks and header methods, processed in R and then saved again to an MS file providing the (eventually) manipulated spectra and header data with arguments header and data.

Usage

  copyWriteMSData(object, file, original_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.
original_file	character(1) with the name of the original file from which the spectrum data was first read.
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.

Note

copyWriteMSData supports at present copying data from mzXML and mzML and exporting to mzML. Copying and exporting to mzXML can fail for some input files.

The intention of this function is to copy data from an existing file and save it along with eventually modified data to a new file. To write new MS data files use the writeMSData function instead.

Author(s)

Johannes Rainer

See Also

writeMSData for a function to save MS data to a new mzML or mzXML 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
})

## Copy metadata and additional information from the originating file
## and save it, along with the modified data, to a new mzML file.
out_file <- tempfile()
copyWriteMSData(pks, file = out_file, original_file = fl,
    header = hdr)

sneumann/mzR documentation built on Nov. 14, 2024, 3:27 a.m.