SegmentedAlleleBFractions     package:aroma.core     R Documentation

_T_h_e _S_e_g_m_e_n_t_e_d_A_l_l_e_l_e_B_F_r_a_c_t_i_o_n_s _c_l_a_s_s

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

     Package:  aroma.core 
      *Class SegmentedAlleleBFractions*

     'Object'
      '~~|'
      '~~+--''RawGenomicSignals'
      '~~~~~~~|'
      '~~~~~~~+--''RawAlleleBFractions'
      '~~~~~~~~~~~~|'
      '~~~~~~~~~~~~+--''SegmentedGenomicSignalsInterface'
      '~~~~~~~~~~~~~~~~~|'
      '~~~~~~~~~~~~~~~~~+--''SegmentedAlleleBFractions'

     *Directly known subclasses:*


     public static class *SegmentedAlleleBFractions*
      extends SegmentedGenomicSignalsInterface

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

     SegmentedAlleleBFractions(..., states=NULL)

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

     ...: Arguments passed to 'RawAlleleBFractions'.

  states: A 'function' returning the copy-number states given a
          'vector' of locus positions.

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

     *Methods:*
      _No methods defined_.

     *Methods inherited from SegmentedGenomicSignalsInterface*:
      as.data.frame, binnedSmoothingByState, extractSubsetByState,
     getStateColorMap, getStateColors, getStates, getUniqueStates,
     kernelSmoothingByState, plot, points, setStateColorMap, setStates

     *Methods inherited from RawAlleleBFractions*:
      extractRawMirroredAlleleBFractions, plot

     *Methods inherited from RawGenomicSignals*:
      addBy, addLocusFields, append, applyBinaryOperator,
     as.data.frame, binnedSmoothing, divideBy,
     estimateStandardDeviation, extractDataForSegmentation,
     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/>)

