addDerivedData            package:RMAGEML            R Documentation

_A_d_d_i_n_g _a  _d_e_r_i_v_e_d _d_a_t_a_s_e_t _t_o _a_n _e_x_i_s_t_i_n_g _M_A_G_E_M_L _d_o_c_u_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

     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 )

_A_r_g_u_m_e_n_t_s:

    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)

_A_u_t_h_o_r(_s):

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

_R_e_f_e_r_e_n_c_e_s:

     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.

_S_e_e _A_l_s_o:

     'importMAGEOM','writeMAGEML'

_E_x_a_m_p_l_e_s:

     #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)

