readMageDesign {MAGEML}R Documentation

Wrapper function for reading MAGE-ML documents

Description

The function readMageDesign is a wrapper function for reading MAGE-ML documents. It returns objects of the classes marrayLayout and marrayInfo.

Usage

readMageDesign(file = NULL, datadir = ".",  fArrayDesign = NULL, fBioAssayData = NULL, fDesignElement = NULL, fBioSequence = NULL, ngc=4, skip=0, sep="\t",quote="",...)

widget.readMageDesign(skip=0, sep="\t",quote="",...)

Arguments

fArrayDesign Filename of XML document containing the ArrayDesign package.
fBioAssayData Filename of XML document containing the BioAssayData package.
fDesignElement Filename of XML document containing the DesignElement package.
fBioSequence Filename of XML document containing the BioSequence package.
file Filename of XML document when the ArrayDesign, BioassayData and DesignElement package are all in one XML file.
datadir Directory containing the XML document
ngc The number of grid columns on your array; the default is 4.
... Further arguments for the `scan' function
skip Further arguments for the `scan' function
quote Further arguments for the `scan' function
sep Further arguments for the `scan' function

Details

This function executes an event based XML parsing. Depending on whether the ArrayDesign, BioAssayData and DesignElement package are in one file or not, three different files will be parsed or only one.

Value

A marrayLayout an a marrayInfo object, named layout and info.

Author(s)

Joke Allemeersch, http://www.esat.kuleuven.ac.be/~jallemee
Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck.

References

Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr and Brazma A. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 2002 Aug 23;3(9):RESEARCH0046.

See Also

getBioAssayData, getDesignElement,getArrayDesign.

Examples

data <- system.file("data", package="MAGEML")
readMageDesign(file = "Iron.xml", datadir = data)
#To call the widget, you use:
if(interactive()){
widget.readMageDesign()
}

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