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, cdf = NULL, xy.offset = NULL)
     indices2xy(i, nr = NULL, cel = NULL, abatch = NULL, cdf = NULL, xy.offset = 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' 

     cdf: character - the name of the corresponding cdf package

xy.offset: an eventual offset for the XY coordinates. See Details

_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'.

     The parameter 'xy.offset' is there for compatibility. For
     historical reasons, the xy-coordinates for the features on
     Affymetrix chips were decided to start at 1 (one) rather than 0
     (zero). One can set the offset to 1 or to 0. Unless the you
     _really_ know what you are doing, it is advisable to let it at the
     default value 'NULL'. This way the package-wide option 'xy.offset'
     is always used.

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

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

_W_a_r_n_i_n_g:

     Even if one really knows what is going on, playing with the
     parameter 'xy.offset' could be risky. Changing the package-wide
     option 'xy.offset' appears much more sane.

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

     L.

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

     'indexProbes'

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

     if (require(affydata)) {
       data(Dilution)
       pm.i <- indexProbes(Dilution, which="pm", genenames="AFFX-BioC-5_at")[[1]]
       mm.i <- indexProbes(Dilution, which="mm", genenames="AFFX-BioC-5_at")[[1]]

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

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

