asExprSet               package:Ringo               R Documentation

_c_o_n_v_e_r_t_s _a _R_i_n_g_o _M_A_L_i_s_t _i_n_t_o _a_n _E_x_p_r_e_s_s_i_o_n_S_e_t

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

     Function to convert an object of class 'MAList' into an object of
     class 'ExpressionSet'. Note that the otherwise optional 'targets'
     component is required in this case to generate the 'phenoData' of
     the new 'ExpressionSet'.

_U_s_a_g_e:

     asExprSet(from, idColumn="PROBE_ID")

_A_r_g_u_m_e_n_t_s:

    from: object of class 'MAList' to convert into an 'ExpressionSet'

idColumn: string; indicating which column of the 'genes' data.frame of
          the MAList holds the identifier for reporters on the
          microarray. This column, after calling 'make.names' on it,
          will make up the unique 'featureNames' of the resulting
          'ExpressionSet'.

_V_a_l_u_e:

     an object of class 'ExpressionSet'

_N_o_t_e:

     There is a more general function for converting MALists to
     ExpressionSets in the package 'convert'. This function here is
     solely intended for converting Ringo-generated 'MAList's into
     'ExpressionSet's.

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

     Joern Toedling

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

     'ExpressionSet', 'preprocess'

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

       exDir <- system.file("exData",package="Ringo")
       exRG  <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)
       exMA  <- preprocess(exRG, "none", returnMAList=TRUE)
       exX   <- asExprSet(exMA)

