CopyNumberSegmentationModel    package:aroma.core    R Documentation

_T_h_e _C_o_p_y_N_u_m_b_e_r_S_e_g_m_e_n_t_a_t_i_o_n_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 CopyNumberSegmentationModel*

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

     *Directly known subclasses:*
      CbsModel, GladModel, HaarSegModel

     public abstract static class *CopyNumberSegmentationModel*
      extends _CopyNumberChromosomalModel_

     This _abstract_ class represents a copy-number segmentation model.

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

     CopyNumberSegmentationModel(...)

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

     ...: Arguments passed to constructor 'CopyNumberChromosomalModel'.

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

     *Methods:*

         'fit'                         Fits the model.
         '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/>)

