R: Reads recursively mass spectrometry data in mzXML format.

readMzXmlDir {readMzXmlData} | R Documentation

## Reads recursively mass spectrometry data in mzXML format.

### Description

Reads recursively all mass spectrometry data in mzXML format in a specified directory.

### Usage

    readMzXmlDir(mzXmlDir, removeCalibrationScans = TRUE,
      removeMetaData = FALSE, rewriteNames = TRUE, fileExtension = "mzXML",
      verbose = FALSE)

### Arguments

`mzXmlDir` | `character`, path to directory which should be read recursively.
`removeCalibrationScans` | `logical`, if `TRUE` all scans in directories called “[Cc]alibration” will be ignored.
`removeMetaData` | `logical`, to save memory metadata could be deleted.
`rewriteNames` | `logical`, if `TRUE` all list elements get an unique name from metadata otherwise file path is used.
`fileExtension` | `character`, file extension of mzXML formatted files. The directory is only searched for fileExtension files. In most cases it would be “"mzXML"” but sometimes you have to use “xml”.
`verbose` | `logical`, verbose output?

### Details

See `readMzXmlFile`.

### Value

A list of spectra.

- `[[1]]spectrum$mass`: A vector of calculated mass.

- `[[1]]spectrum$intensity`: A vector of intensity values.

- `[[1]]metaData`: A list of metaData depending on read spectrum.

### Author(s)

Sebastian Gibb mail@sebastiangibb.de

### See Also

`readMzXmlFile`, `importMzXml`

### Examples

    ## load library
    library("readMzXmlData")

    ## get examples directory
    exampleDirectory <- system.file("Examples", package="readMzXmlData")

    ## read example spectra
    spec <- readMzXmlDir(exampleDirectory)

    ## plot spectra
    plot(spec[[1]]$spectrum$mass, spec[[1]]$spectrum$intensity, type="n")

    l <- length(spec)
    legendStr <- character(l)
    for (i in seq(along=spec)) {
      lines(spec[[i]]$spectrum$mass, spec[[i]]$spectrum$intensity, type="l",
            col=rainbow(l)[i])
      legendStr[i] <- basename(spec[[i]]$metaData$file)
    }

    ## draw legend
    legend(x="topright", legend=legendStr, col=rainbow(l), lwd=1)

[Package readMzXmlData version 2.8.1 Index]