readMSIData {Cardinal}R Documentation

Read mass spectrometry imaging data files

Description

Read supported mass spectrometry imaging data files. Supported formats include imzML and Analyze 7.5.

Usage

## 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"), ...)

Arguments

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 matter on-disk matrix for reading on-demand, rather than loading the data into memory.

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="ppm", this is the half-binwidth, and should be set to the native accuracy of the mass spectrometer, if known. For units="mz", this is simply the step size between m/z bins.

units

The units for resolution. Either parts-per-million or absolute m/z units.

as

After reading in the data, what class of object should be returned (MSImageSet or MSImagingExperiment)?

BPPARAM

An optional instance of BiocParallelParam. See documentation for bplapply. This is only used when mass.range=NULL and attach.only=TRUE, when reading the mass range from the m/z data.

...

Additional arguments passed to read functions.

Details

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.

Value

A MSImageSet object.

Author(s)

Kylie A. Bemis

References

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

See Also

writeMSIData


[Package Cardinal version 2.2.0 Index]