readMSIData: 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=FALSE,
	mass.accuracy=200, units.accuracy=c("ppm", "mz"), ...)
## Read Analyze 7.5 files
readAnalyze(name, folder=getwd(), attach.only=FALSE, ...)

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 Binmat on-disk matrix for reading on-demand, rather than loading the data into memory. This feature is still experimental.

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.

Value

A MSImageSet object.

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 currently supports reading and returning the 'continuous' and 'processed' formats. Note that support for the 'processed' format was added in version 1.3.0 and is still considered experimental and under development.

References