RawGenomicSignals         package:aroma.core         R Documentation

_T_h_e _R_a_w_G_e_n_o_m_i_c_S_i_g_n_a_l_s _c_l_a_s_s

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

     Package:  aroma.core 
      *Class RawGenomicSignals*

     'Object'
      '~~|'
      '~~+--''RawGenomicSignals'

     *Directly known subclasses:*
      RawAlleleBFractions, RawCopyNumbers, RawMirroredAlleleBFractions,
     RawSequenceReads, SegmentedAlleleBFractions, SegmentedCopyNumbers

     public static class *RawGenomicSignals*
      extends Object

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

     RawGenomicSignals(y=NULL, x=NULL, w=NULL, chromosome=NA, name=NULL, ...)

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

       y: A 'numeric' 'vector' of length J specifying the signal at
          each locus.

       x: A (optional) 'numeric' 'vector' of length J specifying the
          position of each locus.

       w: A (optional) non-negative 'numeric' 'vector' of length J
          specifying a weight of each locus.

chromosome: An (optional) 'integer' specifying the chromosome for these
          genomic signals.

    name: An (optional) 'character' string specifying the sample name.

     ...: Not used.

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

     *Methods:*

         'addBy'                      -
         'addLocusFields'             -
         'append'                     -
         'as.data.frame'              -
         'binnedSmoothing'            -
         'divideBy'                   -
         'estimateStandardDeviation'  Estimates the standard deviation of the raw Ys.
         'extractRegion'              -
         'extractSubset'              -
         'gaussianSmoothing'          -
         'getChromosome'              -
         'getLocusFields'             -
         'getName'                    -
         'getPositions'               -
         'getSigma'                   -
         'getSignals'                 -
         'getWeights'                 -
         'getXScale'                  -
         'getXY'                      -
         'getYScale'                  -
         'hasWeights'                 -
         'kernelSmoothing'            -
         'lines'                      -
         'multiplyBy'                 -
         'nbrOfLoci'                  -
         'plot'                       -
         'points'                     -
         'setLocusFields'             -
         'setName'                    -
         'setSigma'                   -
         'setWeights'                 -
         'setXScale'                  -
         'setYScale'                  -
         'signalRange'                -
         'sort'                       -
         'subtractBy'                 -
         'summary'                    -
         'xMax'                       -
         'xMin'                       -
         'xRange'                     -
         'xSeq'                       -
         'yMax'                       -
         'yMin'                       -
         'yRange'                     -

     *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/>)

