CbsModel             package:aroma.core             R Documentation

_T_h_e _C_b_s_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 CbsModel*

     'Object'
      '~~|'
      '~~+--''ChromosomalModel'
      '~~~~~~~|'
      '~~~~~~~+--''CopyNumberChromosomalModel'
      '~~~~~~~~~~~~|'
      '~~~~~~~~~~~~+--''CopyNumberSegmentationModel'
      '~~~~~~~~~~~~~~~~~|'
      '~~~~~~~~~~~~~~~~~+--''CbsModel'

     *Directly known subclasses:*


     public static class *CbsModel*
      extends _CopyNumberSegmentationModel_

     This class represents the Circular Binary Segmentation (CBS) model
     [1].

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

     CbsModel(cesTuple=NULL, ...)

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

cesTuple: A 'CopyNumberDataSetTuple'.

     ...: Arguments passed to the constructor of
          'CopyNumberSegmentationModel'.

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

     *Methods:*

         'getFitFunction'  -

     *Methods inherited from CopyNumberSegmentationModel*:
      fit, getAsteriskTags, getFitFunction, getFullNames, getRegions,
     getTags, plot, plotCopyNumberRegionLayers, writeRegions

     *Methods inherited from CopyNumberChromosomalModel*:
      as.character, calculateChromosomeStatistics, calculateRatios,
     clearCache, estimateSds, extractRawCopyNumbers, fit,
     getDataFileMatrix, getNames, getPairedNames, getReferenceSetTuple,
     getRefSetTuple, isPaired, newPlot, 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

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

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

_R_e_f_e_r_e_n_c_e_s:

     [1] Olshen, A. B., Venkatraman, E. S., Lucito, R., Wigler, M.
     _Circular binary segmentation for the analysis of array-based DNA
     copy number data. Biostatistics 5: 557-572, 2004._
      [2] Venkatraman, E. S. & Olshen, A. B. _A faster circular binary
     segmentation algorithm for the analysis of array CGH data_.
     Bioinformatics, 2007.

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

     'CopyNumberSegmentationModel'.

