extractProbeAnno            package:Ringo            R Documentation

_B_u_i_l_d _p_r_o_b_e_A_n_n_o _f_r_o_m _m_a_t_c_h _p_o_s_i_t_i_o_n_s _i_n _a_n _R_G_L_i_s_t

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

     This function can be used to build a probeAnno object from the
     reporter match positions given in the  'genes' slot of an RGList
     if present, as is the case with some ChIP-chip microarray
     platforms, e.g. with certain Agilent ones after reading in the
     data with 'read.maimages(...,"agilent")'.

_U_s_a_g_e:

     extractProbeAnno(object, format = "agilent", ...)

_A_r_g_u_m_e_n_t_s:

  object: an object that holds the data and the probe match positions,
          currently can only be of class 'RGList'

  format: in which format are the reporter match positions stored in
          the object; see details; currently only "agilent" is
          implemented

     ...: further arguments that are passed on to the function
          'posToProbeAnno'

_D_e_t_a_i_l_s:

     Which information is used for creating the probeAnno is specified
     by the argument 'format'.

     _a_g_i_l_e_n_t expects that the object is of class 'RGList'. The 'genes'
          element of the object is taken. This element is expected to
          have at least a column 'ProbeName', which stores the unique
          reporter/probe identifiers, and a column 'SystematicName',
          which holds the probe match position in the format
          "chr<chromosome>:coordinate1-coordinate2",
          e.g."chr1:087354051-087354110".


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

     An object of  class 'probeAnno' holding the mapping between
     reporters and genomic positions.

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

     Joern Toedling toedling@ebi.ac.uk

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

     'posToProbeAnno', 'probeAnno-class'

