xcmsFragments-class           package:xcms           R Documentation

_C_l_a_s_s _x_c_m_s_F_r_a_g_m_e_n_t_s, _a _c_l_a_s_s _f_o_r _h_a_n_d_l_i_n_g _T_a_n_d_e_m _M_S _a_n_d _M_S$^_n$ _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     This class is similar to 'xcmsSet' because it stores peaks from a
     number of individual files. However,  xcmsFragments keeps Tandem
     MS and e.g. Ion Trap or Orbitrap MS$^n$ peaks, including the
     parent ion relationships.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created with the 'xcmsFragments' constructor and
     filled with peaks using the collect method.

_S_l_o_t_s:


     '_p_e_a_k_s': matrix with colmns peakID (MS1 parent in corresponding
          xcmsSet), MSnParentPeakID (parent peak within this
          xcmsFragments), msLevel (e.g. 2 for Tandem MS), rt (retention
          time in case of LC data), mz (fragment mass-to-charge),
          intensity (peak intensity as reported by XXX), sample (The ID
          of the rawData-file).


_M_e_t_h_o_d_s:


     _c_o_l_l_e_c_t 'signature(object = "xcmsFragments")': gets a
          xcmsSet-object, collects ms1-peaks from it and the msn-peaks
          from the corresponding xcmsRaw-files.

     _p_l_o_t_T_r_e_e 'signature(object = "xcmsFragments")': prints a (text
          based) pseudo-tree of the peaktable to display the
          dependencies of the peaks among each other.

     _s_h_o_w 'signature(object = "xcmsFragments")': print a human-readable
          description of this object to the console.


_N_o_t_e:

     No notes yet.

_A_u_t_h_o_r(_s):

     S. Neumann, J. Kutzera

_R_e_f_e_r_e_n_c_e_s:

     A parallel effort in metabolite profiling data sharing: <URL:
     http://metlin.scripps.edu/>

_S_e_e _A_l_s_o:

     'xcmsRaw'

