readBrukerFlexDir {readBrukerFlexData}

Reads recursively mass spectrometry data in Bruker Daltonics XMASS format.

Description

This function leads recursively all mass spectrometry data in Bruker Daltonics XMASS format in a specified directory.

Usage

readBrukerFlexDir(
  brukerFlexDir,
  removeCalibrationScans = TRUE,
  removeMetaData = FALSE,
  useHpc = TRUE,
  useSpectraNames = TRUE,
  filterZeroIntensities = FALSE,
  verbose = FALSE
)

Arguments

brukerFlexDir

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 calculate mass data a lot of meta data are needed. To save memory they could be deleted after calculation.

useHpc

logical, should Bruker Daltonics' High Precision Calibration be used if available? (see also: .hpc)

useSpectraNames

logical, if TRUE all list elements get an unique name from metaData otherwise file path is used. (If ‘removeMetaData’ is TRUE ‘useSpectraNames’ has no effect.)

filterZeroIntensities

logical, don't change it. If TRUE all intensities equal 0.0 are removed. (see also: readBrukerFlexFile)

verbose

logical, print verbose messages?

Details

See readBrukerFlexFile.

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.

See Also

importBrukerFlex, readBrukerFlexFile, .hpc

Examples

## load library
library("readBrukerFlexData")

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

## read example spectra
spec <- readBrukerFlexDir(file.path(exampleDirectory,
  "2010_05_19_Gibb_C8_A1"))

## 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] <- spec[[i]]$metaData$fullName
}

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