addNormToMAGEML {RMAGEML}R Documentation

Adding a norm object to an existing MAGEML document

Description

This function adds normalised data object obtained with limma or marray package to a MAGEML document.

Usage

addNormToMAGEML(mageOM = NULL, norm = NULL, outputDirectory = ".",
externalDataFiles = NULL, protocolID = NULL, protocol = "none", date="NA", qtID =
NULL, qtName = NULL, qtScale = NULL, qtDataType = NULL, qtDimID =
NULL,transformationID = NULL, DED = "none", BADIDs = NULL, derivedBioAssayIDs = NULL, derivedBioAssayDataIDs = NULL)

Arguments

norm Normalised limma (MAList) or marray (marrayNorm) object
mageOM Reference to MAGE Object Model, generated by importMAGEOM() method.
outputDirectory Directory where updated MAGEML document will be written to
externalDataFiles List of names for external data files associated with a DerivedBioAssayData object. Each filename should end with .txt as this is the standard output file format
protocolID ID you want to give to the protocol, e.g. P-normalised-1
protocol Describiption of the used protocol
date Date when protocol was applied
qtID Identifier used for the QuantitationType (the normalised value)
qtName Name for the QuantitationType
qtScale Scale of the QuantitationType, e.g. linear
qtDataType DataType of the QuantitationType e.g. scalar
qtDimID A new QuantitationTypeDimension will be generated you'll have to specify it's identifier
transformationID Identifier for the applied transformation e.g. TFM:1
DED DesignElementDimension corresponding to the features that are present in the normalised object, if only one dimension present in original MAGEML file then this parameter should not be specified
BADIDs List of BioAssayData identifier
derivedBioAssayIDs List of identifiers for the DerivedBioAssay e.g. DBA-1
derivedBioAssayDataIDs List of identifiers for the DerivedBioAssayData

Author(s)

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

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

importMAGEOM,writeMAGEML

Examples

#library(RMAGEML)
#raw<- importMAGEML(directory = "/home/steffen/data/MEXP-14")
#norm<-maNorm(raw)
#mageom <- importMAGEOM(directory = "/home/steffen/data/MEXP-14")
#outputDirectory <- "/home/steffen/XMLout"
#externalDataFile <- "deriv_test.txt"
#protocolID <- "P-CAGE-test"
#protocol <- "This is a test protocol! Applied maNorm."
#qtID <- c("esat.kuleuven.ac.be:quantT-1-test", "esat.kuleuven.ac.be:quantT-2-test")
#qtName <- c("quantitation Name 1", "quantitation Name 2")
#qtScale <- c("linear","linear")
#qtDataType <- c("scalar","scalar")
#qtDimID <- "esat.kuleuven.ac.be:QTD-test"
#BADIDs <- c("esat.kuleuven.ac.be:BAD-test1","esat.kuleuven.ac.be:BAD-test2")
#derivedBioAssayIDs <- c("esat.kuleuven.ac.be:DBA-test1","esat.kuleuven.ac.be:DBA-test2")
#derivedBioAssayDataIDs <- c("esat.kuleuven.ac.be:DBD-test1", "esat.kuleuven.ac.be:DBD-test2")
#addNormToMAGEML(mageOM = mageom, norm = norm, outputDirectory = outputDirectory, externalDataFile = externalDataFile, protocolID = protocolID, protocol = protocol,  qtID = qtID, qtName = qtName, qtScale = qtScale, qtDataType = qtDataType, qtDimID = qtDimID, DED = "none", BADIDs = BADIDs, derivedBioAssayIDs = derivedBioAssayIDs, derivedBioAssayDataIDs = derivedBioAssayDataIDs)


[Package RMAGEML version 2.1.0 Index]