fillPeaks-methods            package:xcms            R Documentation

_I_n_t_e_g_r_a_t_e _a_r_e_a_s _o_f _m_i_s_s_i_n_g _p_e_a_k_s

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

     For each sample, identify peak groups where that sample is not
     represented. For each of those peak groups, integrate the signal
     in the region of that peak group and create a new peak.

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

  object: the 'xcmsSet' object

  method: the filling method

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

     After peak grouping, there will always be peak groups that do not
     include peaks from every sample. This method produces intensity
     values for those missing samples by integrating raw data in peak
     group region. According to the type of raw-data there are 2
     different  methods available. for filling gcms/lcms data the
     method "chrom" integrates  raw-data in the chromatographic domain,
     whereas "MSW" is used for   peaklists without retention-time
     information like those from  direct-infusion spectra.

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

     A 'xcmsSet' objects with filled in peak groups.

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_x_c_m_s_S_e_t" 'fillPeaks(object, method="")'


_S_e_e _A_l_s_o:

     'xcmsSet-class', 'getPeaks'

