readBrukerFlexDir: Reads recursively mass spectrometry data in Bruker Daltonics' XMASS format.

Description

Reads 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

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 delete 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?

Value

A list of spectra.
[[1]]$spectrum$massA vector of calculated mass.
[[1]]$spectrum$intensityA vector of intensity values.
[[1]]$metaDataA list of metaData depending on read spectrum.

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);