findPeaks-methods            package:xcms            R Documentation

_F_e_a_t_u_r_e _d_e_t_e_c_t_i_o_n _i_n _t_h_e _c_h_r_o_m_a_t_o_g_r_a_p_h_i_c _t_i_m_e _d_o_m_a_i_n

_D_e_s_c_r_i_p_t_i_o_n:

_A_r_g_u_m_e_n_t_s:

  object: 'xcmsSet' object

    fwhm: full width at half maximum of matched filtration gaussian
          model peak 

   sigma: standard deviation of matched filtration model peak 

     max: maximum number of peaks per extracted ion chromatogram 

snthresh: signal to noise ratio cutoff

    step: step size to use for profile generation

   steps: number of steps to merge prior to filtration

  mzdiff: minimum difference in m/z for peaks with overlapping
          retention times 

   index: return indicies instead of values for m/z and retention times 

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

_V_a_l_u_e:

     A matrix with columns: 

       i: rank of peak identified in merged EIC (<= 'max') 

      mz: weighted (by intensity) mean of peak m/z across scans 

   mzmin: m/z of minimum step 

   mzmax: m/z of maximum step 

     ret: retention time of peak midpoint 

  retmin: leading edge of peak retention time 

  retmax: trailing edge of peak retention time 

    into: integrated area of original (raw) peak 

    intf: integrated area of filtered peak 

    maxo: maximum intensity of original (raw) peak 

    maxf: maximum intensity of filtered peak 

_M_e_t_h_o_d_s:

     _o_b_j_e_c_t = "_x_c_m_s_R_a_w" ' findPeaks(object, fwhm = 30, sigma =
          fwhm/2.3548, max = 5,  snthresh = 10, step = 0.1, steps = 2,
          mzdiff = 0.8 - step*steps,  index = FALSE, sleep = 0) '

_S_e_e _A_l_s_o:

     'xcmsRaw-class'

