addDerivedData {RMAGEML}R Documentation

Adding a derived dataset to an existing MAGEML document

Description

This function adds a derived dataset to an existing MAGEML document.

Usage

addDerivedData(mageOM = NULL, data = NULL, outputDirectory = ".", externalDataFile = NULL, protocolID = NULL, protocol = "none", date="NA", qtIDs = NULL, qtNames = NULL, qtScales = NULL, qtDataTypes = NULL, qtDimID = NULL,transformationID=NULL, DED = "none", BAD = NULL, derivedBioAssayID = NULL, derivedBioAssayDataID = NULL, MBA = NULL )

Arguments

data Numeric vector or martix in which the columns corresepond to the derived data one wants to add and the rows correspond to one DesignElementDimension present in the original MAGEML document
mageOM Reference to MAGE Object Model, generated by importMAGEOM() method.
outputDirectory Directory where updated MAGEML document will be written to
externalDataFile Name for external data file associated with a DerivedBioAssayData object. the 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
qtIDs List of identifiers used for the QuantitationTypes. Order should be the same as the columns of the data matrix
qtNames List of names for the QuantitationTypes. Order should be the same as in the qtIDs list and as the columns of the data matrix.
qtScales Scales of the QuantitationType, e.g. linear. Order should be the same as in the qtIDs list and as the columns of the data matrix.
qtDataTypes DataTypes of the QuantitationType e.g. scalar. Order should be the same as in the qtIDs list and as the columns of the data matrix.
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 selected during MAGEML import. If only one dimension present in original MAGEML file then this parameter should not be specified
BAD BioAssayData identifier
derivedBioAssayID Identifier for the DerivedBioAssay e.g. DBA-1
derivedBioAssayDataID Identifier for the DerivedBioAssayData
MBA Location of the MeasuredBioAssays used to generate the DerivedBioAssayData as present in the raw created by import from a MAGEML document. e.g. if first and third hybridisation of a marrayRaw or RGList object were dyeswaps and a combined measure from these two observations was derived, MBA should be a list of length two with values MBA<-c(1,3)

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)
#mageom <- importMAGEOM(directory = "/home/steffen/data/MEXP-14")
#data1 <- rep(1, 960); #dummy dataset
#data <- cbind(data1, data1) #dummy dataset
#outputDirectory <- "/home/steffen/XMLout"
#magemlFile <- "RMAGEMLtest.xml"
#derivedFile <- "deriv_test.txt"
#protocolID <- "P-CAGE-test"
#protocol <- "This is a test protocol! Applied Anova to the raw signal intesities. Flags are set where foreground signal was below background"
#qtIDs <- c("esat.kuleuven.ac.be:quantT-1-test", "esat.kuleuven.ac.be:quantT-2-test")
#qtNames <- c("quantitation Name 1", "quantitation Name 2")
#qtScales <- c("linear","linear")
#qtDataTypes <- c("scalar","scalar")
#qtDimID <- "esat.kuleuven.ac.be:QTD-test"
#BAD <- "esat.kuleuven.ac.be:BAD-test"
#derivedBioAssayID <- "esat.kuleuven.ac.be:DBA-test"
#derivedBioAssayDataID <- "esat.kuleuven.ac.be:DBD-test"
#MBA <- c(0, 2)
#addDerivedData(mageOM = mageom, data = data, outputDirectory = outputDirectory, externalDataFile = externalDataFile, protocolID = protocolID, protocol = protocol,  qtIDs = qtIDs, qtNames = qtNames, qtScales = qtScales, qtDataTypes = qtDataTypes, qtDimID = qtDimID, DED = "none", BAD = BAD, derivedBioAssayID = derivedBioAssayID, derivedBioAssayDataID = derivedBioAssayDataID, MBA = MBA)


[Package RMAGEML version 2.1.0 Index]