coerce                package:convert                R Documentation

_C_o_n_v_e_r_t _D_a_t_a _O_b_j_e_c_t_s

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

     Convert between limma, marray and Biobase data objects.

_D_e_t_a_i_l_s:

     Objects can be converted (coerced) from one class to another using
     'as(object, Class)' where 'object' is an object to convert and
     'Class' is the name of the class to convert to.  The following
     conversions are provided:

       From:         To:
       'RGList'      'marrayRaw'
       'marrayRaw'   'RGList'
       'MAList'      'marrayNorm'
       'marrayNorm'  'MAList'
       'RGList'      'NChannelSet'
       'marrayRaw'   'NChannelSet'
       'MAList'      'ExpressionSet'
       'marrayNorm'  'ExpressionSet'
       Deprecated    
       'RGList'      'exprSet'
       'MAList'      'exprSet'
       'marrayRaw'   'exprSet'

     'RGList' and 'marrayRaw' are coerced to 'NChannelSet'. Channel
     values are not transformed.

     'MAList' and 'marrayNorm' are coerced so that the 'ExpressionSet'
     slot contains log-ratios (M-values) and the 'ExpressionSet' object
     has the same number of columns as the original object.  In this
     case, information on the A-values is lost.

     There is intentionally no conversion from 'RGList' or 'marrayRaw'
     to 'ExpressionSet', as 'ExpressionSet' is intended for expression
     values, not intensities.

     'exprSet' objects are deprecated, but converters to this class
     exist. 'RGList' and 'marrayRaw' objects are coerced to 'exprSet's
     in such a way that green and red channel intensities are stored in
     alternate columns of the 'exprs' slot expression matrix. This
     means that the resulting object has twice as many columns as the
     original object.

_A_u_t_h_o_r(_s):

     Gordon Smyth and others

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

     'as' in the 'methods' package.

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

     ##first set up some fake intensity matrices
     testRed = matrix(rnorm(5*2),5,2, 
       dimnames=list(paste("gene",1:5, sep=""), c("S1", "S2")))
     testGreen = matrix(rnorm(5*2),5,2, 
       dimnames=list(paste("gene",1:5, sep=""), c("S1", "S2")))

     ##some sample/target info
     testTarget = data.frame(slide=c("S1", "S2"), Cy3=c("T", "C"),
       Cy5=c("C", "T"), row.names=c("S1", "S2"))

     maT = new("marrayInfo", maLabels=c("S1", "S2"),
       maInfo= testTarget)

     ##now create instances and convert
     x <- new("RGList")
     x$R = testRed
     x$G = testGreen
     y <- as(x,"marrayRaw")
     z <- as(x, "NChannelSet")

     x <- new("marrayRaw")
     x@maGf <- testGreen
     x@maRf <- testRed
     x@maTargets = maT
     y <- as(x,"RGList")
     z <- as(x, "NChannelSet")

     x <- new("MAList")
     y <- as(x,"marrayNorm")

     ##we construct a reasonably complete fake, small 
     ##instance of the marrayNorm class
     x <- new("marrayNorm")
     x@maM <- testRed
     x@maA <- testGreen
     maTargets(x) = maT
     y <- as(x,"MAList")
     y <- as(x, "ExpressionSet")

     x <- new("MAList")
     x$M <- testRed
     x$A <- testGreen
     x$targets = testTarget
     y <- as(x,"ExpressionSet")

