findPeaks.MSW-methods          package:xcms          R Documentation

_F_e_a_t_u_r_e _d_e_t_e_c_t_i_o_n _f_o_r _s_i_n_g_l_e-_s_p_e_c_t_r_u_m _n_o_n-_c_h_r_o_m_a_t_o_g_r_a_p_h_y _M_S _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     Processing Mass Spectrometry direct-injection spectrum by using
     wavelet based algorithm.

_A_r_g_u_m_e_n_t_s:

  object: 'xcmsSet' object

snthresh: signal to noise ratio cutoff

  scales: scales of CWT

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

   sleep: number of seconds to pause between plotting peak finding
          cycles 

verbose.columns: additional peak meta data columns are returned  

_D_e_t_a_i_l_s:

     This is a wrapper around the peak picker in the bioconductor
     package MassSpecWavelet calling 'cwt', 'get.localMaximum.cwt',
     'get.ridge', 'identify.majorPeaks' and tuneIn.peakInfo.

_V_a_l_u_e:

     A matrix with columns:

      mz: m/z value of the peak at the centroid position 

   mzmin: m/z value at the start-point of the peak 

   mzmax: m/z value at the end-point of the peak 

      rt: always -1 

   rtmin: always -1 

   rtmax: always -1 

    into: integrated area of original (raw) peak 

    maxo: intensity of original (raw) peak at the centroid position 

    intf: always NA  

    maxf: maximum MSW-filter response of the peak 

      sn: Signal/Noise ratio

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_x_c_m_s_R_a_w" ' findPeaks.MSW(object, snthresh=3,
          scales=seq(1,22,3), nearbyPeak=TRUE, peakScaleRange=5,
          amp.Th=0.01, minNoiseLevel=amp.Th/SNR.Th, ridgeLength=24,
          tuneIn=FALSE, sleep=0, verbose.columns = FALSE) '


_A_u_t_h_o_r(_s):

     Steffen Neumann, Joachim kutzera, sneumann|jkutzer@ipb-halle.de

_S_e_e _A_l_s_o:

     'findPeaks-methods' 'xcmsRaw-class' 'peakDetectionCWT'

