tuneInPeakInfo        package:MassSpecWavelet        R Documentation

_T_u_n_e _i_n _t_h_e _p_e_a_k _i_n_f_o_r_m_a_t_i_o_n: _p_e_a_k _p_o_s_i_t_i_o_n _a_n_d _p_e_a_k _s_c_a_l_e

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

     Based on the identified peak position, more precise estimation of
     the peak information, i.e., peak position and peak scale, can be
     got by this function. The basic idea is to cut the segment of
     spectrum near the identified peaks, and then do similar procedures
     as 'peakDetectionCWT', but with more detailed scales around the
     estimated peak scale.

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

     tuneInPeakInfo(ms, majorPeakInfo = NULL, peakIndex = NULL, peakScale = NULL, maxScale = 128, ...)

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

      ms: the mass spectrometry spectrum 

majorPeakInfo: return of 'identifyMajorPeaks' 

peakIndex: the m/z index of the identified peaks

peakScale: the scales of the identified peaks 

maxScale: the maximum scale allowed for the peak 

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

_D_e_t_a_i_l_s:

     The majorPeakInfo or peakIndex and peakScale must be provided.

_V_a_l_u_e:

peakCenterIndex: the updated peak center m/z index

peakScale: the updated peak scale

peakValue: the corresponding peak value

_A_u_t_h_o_r(_s):

     Pan Du

_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:

     'peakDetectionCWT'

_E_x_a_m_p_l_e_s:

             data(exampleMS)
             SNR.Th <- 3
             peakInfo <- peakDetectionCWT(exampleMS, SNR.Th=SNR.Th)
             majorPeakInfo <- peakInfo$majorPeakInfo
             betterPeakInfo <- tuneInPeakInfo(exampleMS, majorPeakInfo)
             plot(500:length(exampleMS), exampleMS[500:length(exampleMS)], type='l', log='x')
             abline(v=betterPeakInfo$peakCenterIndex, col='red')

