writeMSIData {Cardinal} | R Documentation

## Write mass spectrometry imaging data files

### Description

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

### Usage

    ## S4 method for signature 'MSImageSet,character'
    writeMSIData(object, file, outformat=c("imzML", "Analyze"), ...)

    ## S4 method for signature 'MSImageSet'
    writeImzML(object, name, folder=getwd(), merge=FALSE,
    	mz.type="32-bit float", intensity.type="32-bit float", ...)

    ## S4 method for signature 'MSImageSet'
    writeAnalyze(object, name, folder=getwd(),
    	intensity.type="16-bit integer", ...)

### Arguments

`object` | An imaging dataset to be written to file.
`file` | A description of the data file to be write. This may be either an absolute or relative path. Any file extension will be ignored and replaced with an appropriate one.
`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.
`outformat` | The file format to write. Currently, the supported formats are "imzML" or "Analyze".
`merge` | Whether the samples/runs should be written to the same file (`TRUE`) or split into multiple files (`FALSE`). Currently, only `FALSE` is supported.
`mz.type` | The data type for the m/z values. Acceptable values are "32-bit float" and "64-bit float".
`intensity.type` | The data type for the intensity values. Acceptable values are "16-bit integer", "32-bit integer", "64-bit integer", "32-bit float" and "64-bit float".
`...` | Additional arguments passed to write functions.

### Details

The `writeImzML` function supports writing both the 'continuous' and 'processed' formats.

Exporting the metadata is lossy, and not all metadata will be preserved. If exporting an object that was originally imported from an imzML file, any metadata that appears in `metadata()` of the object will be preserved when writing.

Different experimental runs are written to separate files.

The imzML files can be modified after writing (such as to add additional experimental metadata) using the Java-based imzMLValidator application: https://gitlab.com/imzML/imzMLValidator/.

### Value

`TRUE` if the file was written successfully.

### 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

`readMSIData`

[Package Cardinal version 2.12.0 Index]