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 = TRUE, mass.range = NULL, resolution = 200, units = c("ppm", "mz"), as = c("MSImagingExperiment", "MSImageSet"), BPPARAM = bpparam(), ...) ## Read Analyze 7.5 files readAnalyze(name, folder = getwd(), attach.only = TRUE, as = c("MSImagingExperiment", "MSImageSet"), ...)
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.range |
For 'processed' imzML files, the mass range to use for the imported data. If known, providing this can improve the loading time dramatically, as otherwise it is calculated from reading the dataset directly. |
resolution |
For 'processed' imzML files, the accuracy to which the m/z values will be binned after reading. For |
units |
The units for |
as |
After reading in the data, what class of object should be returned ( |
BPPARAM |
An optional instance of |
... |
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.
When attach.only=TRUE
, the data is not loaded into memory; only the experimental metadata is read, and the intensity data will only be accessed on-demand. For large datasets, this is memory-efficient. For smaller datasets, this may be slower than simply reading the entire dataset into memory.
If the mass range is known, setting mass.range
will make reading data much faster for very large datasets.
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