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 currently only supports writing the 'continuous' format. Exporting the metadata is lossy, and not all metadata will be preserved.

### 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 2.2.6 Index]