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'

     '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.

_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")

