CopyNumberChromosomalModel    package:aroma.core    R Documentation

_T_h_e _C_o_p_y_N_u_m_b_e_r_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 CopyNumberChromosomalModel*

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

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

     public abstract static class *CopyNumberChromosomalModel*
      extends _ChromosomalModel_

     This _abstract_ class represents a copy-number model.

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

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

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

cesTuple: A 'CopyNumberDataSetTuple'.

refTuple: An optional 'CopyNumberDataFile', or 'CopyNumberDataSet' or
          'CopyNumberDataSetTuple' for pairwise comparisons.

    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'                -
         'extractRawCopyNumbers'     Extracts relative copy numbers.
         'fit'                       Fits the model.
         'getNames'                  -
         'getReferenceSetTuple'      -
         'isPaired'                  -
         'plotAxesLayers'            -
         'plotChromosomesLayers'     -
         'plotCytobandLayers'        -
         'plotFitLayers'             -
         'plotGridHorizontalLayers'  -
         'plotRawCopyNumbers'        -
         'plotSampleLayers'          -

     *Methods inherited from ChromosomalModel*:
      as.character, clearCache, fit, getAlias, getAsteriskTags,
     getChipType, getChipTypes, getChromosomes, getFullName,
     getFullNames, getGenome, getGenomeData, getGenomeFile,
     getListOfAromaUgpFiles, getName, getNames, getParentPath, getPath,
     getReportPath, getRootPath, getSets, getSetTuple, getTags,
     indexOf, nbrOfArrays, nbrOfChipTypes, 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/>)

