readMSIData {Cardinal} | R Documentation |
Read supported mass spectrometry imaging data files. Supported formats include imzML and Analyze 7.5.
## Read any supported MS imaging file readMSIData(file, ...) ## Read imzML files readImzML(name, folder=getwd(), attach.only=FALSE, mass.accuracy=200, units.accuracy=c("ppm", "mz"), ...) ## Read Analyze 7.5 files readAnalyze(name, folder=getwd(), attach.only=FALSE, ...)
file |
A description of the data file to be read. This may be either an absolute or relative path. The file extension must be included. |
name |
The common file name for the '.imzML' and '.ibd' files for imzML or for the '.hdr', '.t2m', and '.img' files for Analyze 7.5. |
folder |
The path to the folder containing the data files. |
attach.only |
Attach the file as a |
mass.accuracy |
For 'processed' imzML files, the accuracy to which the m/z values will be binned after reading. This should be set to the native accuracy of the mass spectrometer, if known. |
units.accuracy |
The units for 'mass.accuracy'. |
... |
Additional arguments passed to read functions. |
In the current implementation, the file extensions must match exactly: '.imzML' and '.ibd' for imzML and '.hdr', '.t2m', and '.img' for Analyze 7.5.
The readImzML
function supports reading and returning both the 'continuous' and 'processed' formats.
A MSImageSet
object.
Kylie A. Bemis
Schramm T, Hester A, Klinkert I, Both J-P, Heeren RMA, Brunelle A, Laprevote O, Desbenoit N, Robbe M-F, Stoeckli M, Spengler B, Rompp A (2012) imzML - A common data format for the flexible exchange and processing of mass spectrometry imaging data. Journal of Proteomics 75 (16):5106-5110. doi:10.1016/j.jprot.2012.07.026