readBrukerFlexDir: 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
)

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.

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.

Examples

Run this code

## 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)

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