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")
     }

