xy2indices               package:affy               R Documentation

_F_u_n_c_t_i_o_n_s _t_o _c_o_n_v_e_r_t _i_n_d_i_c_e_s _t_o _x/_y (_a_n_d _r_e_v_e_r_s_e)

_D_e_s_c_r_i_p_t_i_o_n:

     Functions to convert indices to x/y (and reverse)

_U_s_a_g_e:

     xy2indices(x, y, nr = NULL, cel = NULL, abatch = NULL)
     indices2xy(i, nr = NULL, cel = NULL, abatch = NULL)

_A_r_g_u_m_e_n_t_s:

       x: 'X' position for the probes 

       y: 'Y' position for the probes 

       i: indices in the 'AffyBatch' for the probes 

      nr: total number of 'Xs' on the chip 

     cel: a corresponding object of class 'Cel' 

  abatch: a corresponding object of class 'AffyBatch' 

_D_e_t_a_i_l_s:

     The probes intensities for given probe set ids are extracted from
     an 'AffyBatch' object using the indices stored in the
     corresponding 'cdfenv'.

_V_a_l_u_e:

     A vector of indices or a two-columns matrix of Xs and Ys.

_A_u_t_h_o_r(_s):

     L.

_S_e_e _A_l_s_o:

     'indexProbes'

_E_x_a_m_p_l_e_s:

     data(affybatch.example)

     pm.i <- indexProbes(affybatch.example, which="pm", genenames="AFFX-BioC-5_at")[[1]]
     mm.i <- indexProbes(affybatch.example, which="mm", genenames="AFFX-BioC-5_at")[[1]]

     pm.i.xy <- indices2xy(pm.i, abatch = affybatch.example)
     mm.i.xy <- indices2xy(mm.i, abatch = affybatch.example)

     image(affybatch.example[1], transfo=log2)
     ## plot the pm in red
     plotLocation(pm.i.xy, col="red")
     plotLocation(mm.i.xy, col="blue")

