readSRMData {MSnbase} | R Documentation |
The readSRMData
function reads MRM/SRM data from provided mzML files and
returns the results as a Chromatograms()
object.
readSRMData(files, pdata = NULL)
files |
|
pdata |
|
readSRMData
supports reading chromatogram entries from mzML files. If
multiple files are provided the same precursor and product m/z for SRM/MRM
chromatograms are expected across files. The number of columns of the
resulting Chromatograms()
object corresponds to the number of files. Each
row in the Chromatograms()
object is supposed to contain chromatograms
with same polarity, precursor and product m/z. If chromatograms with
redundant polarity, precursor and product m/z values are found, they are
placed into multiple consecutive rows in the Chromatograms()
object.
A Chromatograms()
object. See details above for more information.
readSRMData
reads only SRM/MRM chromatogram data, i.e. chromatogram data
from mzML files with precursorIsolationWindowTargetMZ
and
productIsolationWindowTargetMZ
attributes. Total ion chromatogram data is
hence not extracted.
The number of features and hence rows of the resulting Chromatograms
object depends on the total list of unique precursor and product m/z
isolation windows found across all input files. In cases in which not each
file has chromatgraphic data for the same polarity, precursor and product
m/z, an empty Chromatogram()
object is reported for the specific precursor
and product m/z combination of the respective file (and a warning is
thrown).
Johannes Rainer
## Read an example MRM/SRM data library(msdata) fl <- proteomics(full.names = TRUE, pattern = "MRM") ## Read the data mrm <- readSRMData(fl) ## The data is represented as a Chromatograms object, each column ## containing the data from one input file mrm ## Access the polarity for each chromatogram (row) polarity(mrm) ## Access the precursor m/z. The result is returned as a matrix with ## columns representing the minimum and maximum m/z (will be identical in ## most cases). precursorMz(mrm) ## Access the product m/z. productMz(mrm) ## Plot one chromatogram plot(mrm[1, ])