ChromosomalModel         package:aroma.core         R Documentation

_T_h_e _C_h_r_o_m_o_s_o_m_a_l_M_o_d_e_l _c_l_a_s_s

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

     Package:  aroma.core 
      *Class ChromosomalModel*

     'Object'
      '~~|'
      '~~+--'_'ChromosomalModel'_

     *Directly known subclasses:*
      CbsModel, _CopyNumberChromosomalModel_,
     _CopyNumberSegmentationModel_, GladModel, HaarSegModel,
     _RawCopyNumberModel_

     public abstract static class *ChromosomalModel*
      extends Object

     This _abstract_ class represents a chromosomal model.

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

     ChromosomalModel(cesTuple=NULL, tags="*", genome="Human", ...)

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

cesTuple: A 'AromaMicroarrayDataSetTuple'.

    tags: A 'character' 'vector' of tags.

  genome: A 'character' string specifying what genome is process.

     ...: Not used.

_F_i_e_l_d_s _a_n_d _M_e_t_h_o_d_s:

     *Methods:*

         'clearCache'              -
         'fit'                     -
         'getAlias'                -
         'getChipType'             Gets a label for all chip types merged.
         'getChipTypes'            -
         'getChromosomes'          Gets the chromosomes available.
         'getFullName'             -
         'getFullNames'            -
         'getGenome'               -
         'getListOfAromaUgpFiles'  -
         'getName'                 -
         'getNames'                Gets the names of the arrays.
         'getParentPath'           -
         'getPath'                 -
         'getRootPath'             -
         'getSets'                 -
         'getTags'                 -
         'indexOf'                 -
         'nbrOfArrays'             Gets the number of arrays.
         'nbrOfChipTypes'          Gets the number of chip types.
         'setAlias'                -
         'setGenome'               -

     *Methods inherited from Object*:
      asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally,
     clearCache, clone, detach, equals, extend, finalize, gc,
     getEnvironment, getFields, getInstantiationTime,
     getStaticInstance, hasField, hashCode, ll, load, objectSize,
     print, registerFinalizer, save

_R_e_q_u_i_r_e_m_e_n_t_s:

     This class requires genome information annotation files for every
     chip type.

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

     Henrik Bengtsson (<URL: http://www.braju.com/R/>)

