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=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.
`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.

### 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.

### 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 1.12.1 Index]