getPeaks-methods            package:xcms            R Documentation

_G_e_t _p_e_a_k _i_n_t_e_n_s_i_t_i_e_s _f_o_r _s_p_e_c_i_f_i_e_d _r_e_g_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     Integrate extracted ion chromatograms in pre-defined defined
     regions. Return output similar to 'link{findPeaks}'.

_A_r_g_u_m_e_n_t_s:

  object: the 'xcmsSet' object

peakrange: matrix or data frame with 4 columns: 'mzmin', 'mzmax',
          'rtmin', 'rtmax' (they must be in that order or named) 

    step: step size to use for profile generation

_V_a_l_u_e:

     A matrix with columns: 

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

      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, always 'NA' 

    maxo: maximum intensity of original (raw) peak 

    maxf: maximum intensity of filtered peak, always 'NA' 

_M_e_t_h_o_d_s:

     _o_b_j_e_c_t = "_x_c_m_s_R_a_w" 'getPeaks(object, peakrange, step = 0.1)'

_S_e_e _A_l_s_o:

     'xcmsRaw-class'

