CdfEnvAffy-class         package:altcdfenvs         R Documentation

_C_l_a_s_s "_C_d_f_E_n_v_A_f_f_y"

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

     A class to hold the information necessary to handle the grouping
     of probes in set of probes, and to find XY coordinates of probes
     on a chip

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("CdfEnvAffy",
     ...)'. Typically, there is an instance of the class for each type
     of chip (e.g. Hu6800, HG-U95A, etc...).

_S_l_o_t_s:


     '_e_n_v_i_r': Object of class '"environment"'. It has to be thought of
          as a hashtable: the keys are probe set identifiers, or gene
          names, and the values are indexes.

     '_e_n_v_N_a_m_e': Object of class '"character"'. A name for the
          environment.

     '_i_n_d_e_x_2_x_y': Object of class '"function"'. The function used to
          resolve index into xy coordinates. Unless you are an advanced
          user, you probably want to ignore this (and rely on the
          default provided with the package).

     '_x_y_2_i_n_d_e_x': Object of class '"function"'. The function used to
          resolve xy coordinates into index. Unless you are an advanced
          user, you probably want to ignore this (and rely on the
          default provided with the package).

     '_n_r_o_w': Object of class '"integer"'. The number of rows of probes
          for the chip type.

     '_n_c_o_l': Object of class '"integer"'. The number of columns of
          probes for the chip type.

     '_p_r_o_b_e_T_y_p_e_s': Object of class '"character"'. The different types
          of probes stored for each probe set. In the case of {\it
          Affymetrix} chips, the probes are typically perfect match
          (pm) probes or mismatch probes (mm).

     '_c_h_i_p_T_y_p_e': Object of class '"character"'. The name of the chip
          type the instance is associated with. This is useful when one
          starts to create alternative mappings of the probes on a chip
          (see associated vignette).

_M_e_t_h_o_d_s:


     [ 'signature(object = "CdfEnvAffy", i = "character", j =
          "missing", drop = "boolean")': subset a cdf, that is return a
          new cdf containing only a subset of the probe sets. The
          subset of probe sets to take is identified as a vector of
          identifiers (mode "character").

     _c_o_e_r_c_e 'signature(object = "CdfEnvAffy", "environment")': coerce
          an instance of the class to an 'enviroment'.

     _c_o_e_r_c_e 'signature(object = "CdfEnvAffy", "Cdf")': coerce an
          instance of the class to a 'Cdf'.

     _g_e_n_e_N_a_m_e_s 'signature(object="CdfEnvAffy")': Return the names of
          the known probe sets (of course, it depends on the associated
          CDF).

     _i_n_d_e_x_2_x_y 'signature(object = "CdfEnvAffy", i="integer")': convert
          index values into XY coordinates.

     _i_n_d_e_x_P_r_o_b_e_s 'signature(object = "CdfEnvAffy", which = "character",
          probeSetNames = NULL)': obtain the indexes for the probes
          associated wit the probe set name 'probeSetNames'. When
          'probeSetNames' is set to 'NULL' (default), the indexes are
          returned for the probe sets defined on the chip. See
          'indexProbes.CdfEnvAffy'

     _p_l_o_t 'signature(x = "CdfEnvAffy", y = "missing")': Plot the chip.
          It mainly sets coordinates for further plotting (see
          examples). See 'plot.CdfEnvAffy'

     _s_h_o_w 'signature(object = "CdfEnvAffy")': Print method.

     _x_y_2_i_n_d_e_x 'signature(object = "CdfEnvAffy", x="integer",
          y="integer")': convert XY coordinates into index values.

     _t_o_H_y_p_e_r_g_r_a_p_h 'signature(object = "CdfEnvAffy")': convert XY
          coordinates into index values.

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

     Laurent Gautier

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

     'indexProbes.CdfEnvAffy', 'plot.CdfEnvAffy'

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

     ## build an instance
     library(hgu95acdf)
     cdfenv.hgu95a <- wrapCdfEnvAffy(hgu95acdf, 640, 640, "HG-U95A")

     show(cdfenv.hgu95a)

     ## find the indexes for a probe set (pm only)
     ip <- indexProbes(cdfenv.hgu95a, "pm", "1000_at")[[1]]
     ## get the XY coordinates for the probe set
     xy <- index2xy(cdfenv.hgu95a, ip)

     ## plot the chip
     plot(cdfenv.hgu95a)

     ## plot the coordinates
     plotLocation(xy)

     ## subset the environment

     cdfenv.hgu95a.mini <- cdfenv.hgu95a["1000_at"]

