RawSequenceReads         package:aroma.core         R Documentation

_T_h_e _R_a_w_S_e_q_u_e_n_c_e_R_e_a_d_s _c_l_a_s_s

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

     Package:  aroma.core 
      *Class RawSequenceReads*

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

     *Directly known subclasses:*


     public static class *RawSequenceReads*
      extends RawGenomicSignals

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

     RawSequenceReads(x=NULL, y=rep(1, length(x)), ...)

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

       x: An 'integer' 'vector' of length J specifying the read
          positions.

       y: An (optional) 'integer' 'vector' of length J specifying the
          number of reads at each position. Default is one read per
          position.

     ...: Arguments passed to 'RawGenomicSignals'.

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

     *Methods:*

         'binnedSums'             -
         'extractRawCopyNumbers'  -
         'nbrOfReads'             -
         '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/>)

