BrukerParser {WMBrukerParser}R Documentation

Parser for Bruker-Ultraflex TOF Mass Spectrometry Data

Description

This routine reads binary fid Bruker files from a single bioprocessor run, along with associated experimental files and creates R structures, tofList and tofListMetaData.

Usage

BrukerParser(dataSource, dataDirectory)

Arguments

dataSource Typically laboratory where data was obtained
dataDirectory Data directory path.

Details

The BrukerParser routine is called by the ParseAndSave routine using ParserParams$dataSource and the path built from ParserParams$dataDirLeft, ParserParams$runIndices and ParserParams$dataDirRight.

This routine looks for the following contents in the dataDirectory:
1. a subdirectory with “calibration” in the name (optional)
2. a file with the extension .par (optional)
3. a file with the extension .axe (optional)
4. a file with the extension .isset (optional)
5. a file named sample.xml (optional)
6. spot subdirectories with names like 0_A1 and 0_L5 (required), each containing:
EITHER (for Linear TOF data):
/1/1SLin/fid - the binary data file (required)
/1/1SLin/acqu - the acquisition information file (required)
/1/1SLin/pdata/1/proc - the processing file (required)
OR (for Reflector TOF data):
/1/1SRef/fid - the binary data file (required)
/1/1SRef/acqu - the acquisition information file (required)
/1/1SRef/pdata/1/proc - the processing file (required)

Value

tofList A list of time-of-flight mass spectrum vectors addressable by spectrumName.
tofListMetaData A data.frame containing string values for experimental meta-data, with rows and columns addressable by spectrumName and attributeName.

Note

If any of the optional files are missing, the user has the option updating meta-data fields in the parsed meta-data structure, tofListMetaData. If the sample.xml file is missing, a field used in naming data and meta-data structures is missing and placeholders will be used. In this case, the user may wish to update structure names.

If the final line of the .axe file is not blank, R will generate a warning message such as: "In readLines(qq, n = -1) : incomplete final line found in 0-20KDaLin030308.axe" This has no effect on the reader and can be ignored.

Author(s)

William E. Cooke, College of William and Mary, wecook@wm.edu

See Also

WMBrukerParser, ParserParams, ParseAndSave, tofList, tofListMetaData

Examples

dataSource <- "Lab1"

directory = system.file("Examples", package = "WMBrukerParser")
dataDirectory <- 
paste(directory,"/C3ValidationExtractSmall/RobotRun1/2-100kDa",sep="")

BrukerParser(dataSource, dataDirectory)

[Package WMBrukerParser version 1.1 Index]