exprExternal-class       package:exprExternal       R Documentation

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_D_e_s_c_r_i_p_t_i_o_n:

     This is a class representing Microarray Data. Unlike its parent
     class 'exprSet', this class uses reference to an external matrix
     object for storing the gene expression data.

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     Objects can be created by either using
      'as(x, "exprExternal")'
      where 'x' is an object of class 'exprSet' or by a call of the
     form
      '  new('exprExternal','
      '    exprs.ext    = ...., # Object of class
     indirectExternalMatrix'
      '    se.exprs.ext = ...., # Object of class
     indirectExternalMatrix'
      '    phenoData    = ...., # Object of class phenoData'
      '    annotation   = ...., # Object of class character'
      '    description  = ...., # Object of class MIAME'
      '    notes        = ...., # Object of class character'
      '  )'

_S_l_o_t_s:

     '_e_x_p_r_s._e_x_t': Object of class "indirectExternalMatrix". The
          observed expression levels. This contains refernce to an
          object of class 'externalVector' of two dimensions with
          columns representing patients or cases and rows representing
          genes. 

     '_s_e._e_x_p_r_s._e_x_t': Object of class "indirectExternalMatrix". This
          either contains reference to an object of class
          'externalVector' of the same dimensions as 'exprs' which
          contains standard error estimates for the estimated
          expression levels or reference to an object of class
          'externalVector' of length zero. 

     '_p_h_e_n_o_D_a_t_a': Object of class "phenoData" This is an instance of
          class 'phenoData'  containing the patient (or case) level
          data. The columns of the pData slot of this entity represent
          variables and the rows represent patients or cases. 

     '_a_n_n_o_t_a_t_i_o_n' A character string identifying the annotation that
          may be used for the 'exprSet' instance.

     '_d_e_s_c_r_i_p_t_i_o_n': Object of class "MIAME". For compatibility with
          previous version of this class description can also be a
          "character". The clase 'characterOrMIAME' has been defined
          just for this. 

     '_n_o_t_e_s': Object of class "character" Vector of explanatory text 

_M_e_t_h_o_d_s:

     _e_x_p_r_s 'signature(object = "exprExternal")': An accessor function
          for the exprs.ext slot. 

     _s_e._e_x_p_r_s 'signature(object = "exprExternal")': An accessor
          function for the se.exprs.ext slot. 

     _e_x_p_r_s_2_e_x_c_e_l 'signature(x = "exprExternal")': Writes the expression
          levels to 'csv' file. This file will open nicely in excel. It
          takes the same arguments as 'write.table'. If  called with no
          arguments it is equivalent to
          'write.table(force(exprs(exprSet))[,],file="tmp.csv", sep =
          ",", col.names = NA)'.

     _w_r_i_t_e._e_x_p_r_s 'signature(x = "exprExternal")': Writes the expression
          levels to file. It takes the same arguments as 'write.table'.
          If called with no arguments it is equivalent to
          write.table(force(exprs(exprSet))[,],file="tmp.txt",quote=FAL
          SE,sep="\t").

     _c_o_e_r_c_e 'signature(from = "exprSet", to = "exprExternal")': Convert
          an object of class 'exprSet' to an equivalent object of class
          'exprExternal'. This is almost never called directly.
          Instead, use
           'as(exprSet, "exprExternal")'

_S_e_e _A_l_s_o:

     'exprSet-class'

_E_x_a_m_p_l_e_s:

       ## Run the examples from exprSet manual page
       library('externalVector')
       library('Biobase')
       data(geneData)
       data(geneCov)
       covdesc<- list("Covariate 1", "Covariate 2", "Covariate 3")
       names(covdesc) <- names(geneCov)
       pdata <- new("phenoData", pData=geneCov, varLabels=covdesc)
       pdata[1,]
       pdata[,2]

       eset <- as(new("exprSet", exprs=geneData, phenoData=pdata),
                  "exprExternal")
       eset
       eset[,1:10]
       eset[,1]
       eset[1,]
       eset[1,1]
       eset[1:100,]
       eset[1:44,c(2,4,6)]
       Means <- iter(eset, f=mean)

       

       sp1 <- split(eset, c(1,2))
       sp2 <- split(eset, c(rep(1,6), rep(2,7)))

