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'      'exprSet'
       'MAList'      'exprSet'
       'marrayRaw'   'exprSet'
       'marrayNorm'  'exprSet'

     Note that 'RGList' and 'marrayRaw' objects are coerced to
     'exprSet' 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 'exprSet' object has twice as many
     columns as the original object. On the other hand, 'MAList' and
     'marrayNorm' are coerced so that the resulting 'exprs' slot
     contains log-ratios (M-values) and the 'exprSet' object has the
     same number of columns as the original object. In this case,
     information on the A-values is lost.

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

     Gordon Smyth

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

     'as' in the 'methods' package.

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

     x <- new("RGList")
     y <- as(x,"marrayRaw")

     x <- new("marrayRaw")
     x@maGf <- matrix(rnorm(5*2),5,2)
     x@maRf <- matrix(rnorm(5*2),5,2)
     y <- as(x,"RGList")
     y <- as(x,"exprSet")

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

     x <- new("marrayNorm")
     x@maM <- matrix(rnorm(5*2),5,2)
     x@maA <- matrix(rnorm(5*2),5,2)
     y <- as(x,"MAList")
     y <- as(x,"exprSet")

     x <- new("MAList")
     x$M <- matrix(rnorm(5*2),5,2)
     y <- as(x,"exprSet")

