collect-methods             package:xcms             R Documentation

_C_o_l_l_e_c_t _M_S$^_n$ _p_e_a_k_s _i_n_t_o _x_c_m_s_F_r_a_g_m_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Collecting Peaks into 'xcmsFragments's from several MS-runs using
     'xcmsSet' and 'xcmsRaw'.

_A_r_g_u_m_e_n_t_s:

  object: (empty) 'xcmsFragments-class' object

      xs: A 'xcmsSet-class' object which contains picked ms1-peaks from
          several experiments

compMethod: ("floor", "round", "none"): compare-method which is used to
          find the parentpeak of a MSnpeak through comparing the
          MZ-values of the  MS1peaks with the MSnParentPeaks.

snthresh, mzgap, uniq: these are the paramters for the
          getspec-peakpicker included in xcmsRaw.

_D_e_t_a_i_l_s:

     After running collect(xFragments,xSet) The peaktable of the
     xcmsFragments includes the ms1Peaks from all experinemts stored in
     a xcmsSet-object. Further it contains the relevant msN-peaks from
     the xcmsRaw-objects, which were created temporarily with the paths
     in xcmsSet.

_V_a_l_u_e:

     A matrix with columns: 

  peakID: unique identifier of every peak 

MSnParentPeakID: PeakID of the parentpeak of a msLevel>1 - peak, it is
          0 if the peak is msLevel 1. 

 msLevel: The msLevel of the peak. 

      rt: retention time of the peak midpoint 

      mz: the mz-Value of the peak 

intensity: the intensity of the peak 

  sample: the number of the sample from the xcmsSet 

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_x_c_m_s_F_r_a_g_m_e_n_t_s" ' collect(object, ...) '


