peakDetectionCWT       package:MassSpecWavelet       R Documentation

_T_h_e _m_a_i_n _f_u_n_c_t_i_o_n _o_f _p_e_a_k _d_e_t_e_c_t_i_o_n _b_y _C_W_T _b_a_s_e_d _p_a_t_t_e_r_n _m_a_t_c_h_i_n_g

_D_e_s_c_r_i_p_t_i_o_n:

     This function is a wrapper of 'cwt', 'getLocalMaximumCWT',
     'getRidge', 'identifyMajorPeaks'

_U_s_a_g_e:

     peakDetectionCWT(ms, scales = c(1, seq(2, 30, 2), seq(32, 64, 4)), SNR.Th = 3, nearbyPeak = TRUE, peakScaleRange = 5, amp.Th = 0.01, minNoiseLevel = amp.Th/SNR.Th, ridgeLength = 24, tuneIn = FALSE, ...)

_A_r_g_u_m_e_n_t_s:

      ms: the mass spectrometry spectrum 

  scales: scales of CWT 

  SNR.Th: SNR (Signal to Noise Ratio) threshold

nearbyPeak: Determine whether to include the nearby small peaks of
          major peaks. TRUE by default

peakScaleRange: the scale range of the peak. larger than 5 by default. 

  amp.Th: the minimum required amplitude of the peak 

minNoiseLevel: the minimum noise level used in computing the SNR 

ridgeLength: the minimum highest scale of the peak in 2-D CWT
          coefficient matrix 

  tuneIn: determine whether to tune in the parameter estimation of the
          detected peaks 

     ...: other parameters of used by 'getLocalMaximumCWT', 'getRidge',
          'identifyMajorPeaks' 

_V_a_l_u_e:

majorPeakInfo: return of 'identifyMajorPeaks'

ridgeList: return of 'getRidge'

localMax: return of 'getLocalMaximumCWT' 

  wCoefs: 

     { 2-D CWT coefficient matrix, see 'cwt' for details.}

_A_u_t_h_o_r(_s):

     Pan Du, Simon Lin

_R_e_f_e_r_e_n_c_e_s:

     Du, P., Kibbe, W.A. and Lin, S.M. (2006) Improved peak detection
     in mass spectrum by incorporating continuous wavelet
     transform-based pattern matching, Bioinformatics, 22, 2059-2065.

_S_e_e _A_l_s_o:

     'cwt', 'getLocalMaximumCWT', 'getRidge', 'identifyMajorPeaks'

_E_x_a_m_p_l_e_s:

             data(exampleMS)
             SNR.Th <- 3
             peakInfo <- peakDetectionCWT(exampleMS, SNR.Th=SNR.Th)
             majorPeakInfo = peakInfo$majorPeakInfo
             peakIndex <- majorPeakInfo$peakIndex
             plotPeak(exampleMS, peakIndex, main=paste('Identified peaks with SNR >', SNR.Th)) 

