HaarSegModel           package:aroma.core           R Documentation

_T_h_e _H_a_a_r_S_e_g_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 HaarSegModel*

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

     *Directly known subclasses:*


     public static class *HaarSegModel*
      extends _CopyNumberSegmentationModel_

     This class represents the Haar wavelet-based segmentation
     (HaarSeg) model [1].

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

     HaarSegModel(cesTuple=NULL, ..., breaksFdrQ=1e-04)

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

cesTuple: A 'CopyNumberDataSetTuple'.

breaksFdrQ: Default tuning parameters specific to the HaarSeg
          algorithm.

     ...: 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] Ben-Yaacov E. and Eldar YC. _A fast and flexible method for
     the segmentation of aCGH data_, Bioinformatics, 2008. <URL:
     http://www.ee.technion.ac.il/Sites/People/YoninaEldar/Info/software/HaarSeg.htm>

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

     'CopyNumberSegmentationModel'.

