createMaigesRaw          package:maigesPack          R Documentation

_F_u_n_c_t_i_o_n _t_o _c_r_e_a_t_e _o_b_j_e_c_t_s _o_f _c_l_a_s_s _m_a_i_g_e_s_R_a_w

_D_e_s_c_r_i_p_t_i_o_n:

     Function to create objects of class 'maigesRaw' from objects of
     class 'maigesPreRaw'.

_U_s_a_g_e:

     createMaigesRaw(PreRaw, greenDataField, greenBackDataField, redDataField,
                     redBackDataField, flagDataField, gLabelGrp, gLabelPath)

_A_r_g_u_m_e_n_t_s:

  PreRaw: object of class 'maigesPreRaw' to be used to generate another
          object of class 'maigesRaw'.

greenDataField: character string specifying the name of the 'Data' slot
          from 'PreRaw' that will be used to read the spot intensity
          values for green channel.

greenBackDataField: character string specifying the name of the 'Data'
          slot from 'PreRaw' that will be used to read the background
          intensity values for green channel.

redDataField: character string specifying the name of the 'Data' slot
          from 'PreRaw' that will be used to read the spot intensity
          values for red channel.

redBackDataField: character string specifying the name of the 'Data'
          slot from 'PreRaw' that will be used to read the background
          intensity values for red channel.

flagDataField: character string specifying the name of the 'Data' slot
          from 'PreRaw' that will be used to read the flag values.

gLabelGrp: character string with the gene label to match gene groups.

gLabelPath: character string with the gene label to match gene
          networks.

_V_a_l_u_e:

     The result of this function is an object of class 'maigesRaw'.

_A_u_t_h_o_r(_s):

     Gustavo H. Esteves <gesteves@vision.ime.usp.br>

_S_e_e _A_l_s_o:

     'loadData', 'maigesPreRaw',

_E_x_a_m_p_l_e_s:

     ## Load a little dataset
     data(gastro)

     ## See the object
     gastro

     ## Transform gastro into a maigesRaw object
     gastro.raw = createMaigesRaw(gastro, greenDataField="Ch1.Mean",
       greenBackDataField="Ch1.B.Mean", redDataField="Ch2.Mean",
       redBackDataField="Ch2.B.Mean", flagDataField="Flags",
       gLabelGrp="GeneName", gLabelPath="GeneName")

