group.mzClust              package:xcms              R Documentation

_G_r_o_u_p _P_e_a_k_s _v_i_a _H_i_g_h _R_e_s_o_l_u_t_i_o_n _A_l_i_g_n_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     Runs high resolution alignment on the peaks stored in a given
     xcmsSet.

_U_s_a_g_e:

     groupedobject <- group(object, method="mzClust", mzppm = 20, mzabs = 0, minsamp = 1, minsampclass=0, minfrac=0)

_A_r_g_u_m_e_n_t_s:

  object: a xcmsSet with peaks 

   mzppm: the relative error used for clustering/grouping in ppm (parts
          per million)

   mzabs: the absolute error used for clustering/grouping

 minsamp: set the minimum number of samples in one bin

 minfrac: set the minimum fraction of each class in one bin

_V_a_l_u_e:

     Returns a xcmsSet with slots groups and groupindex set.

_R_e_f_e_r_e_n_c_e_s:

     Saira A. Kazmi, Samiran Ghosh, Dong-Guk Shin, Dennis W. Hill and
     David F. Grant
      _Alignment of high resolution mass spectra: development of a
     heuristic approach for metabolomics_.
      Metabolomics, Vol. 2, No. 2, 75-83 (2006)

_S_e_e _A_l_s_o:

     'xcmsSet-class',

_E_x_a_m_p_l_e_s:

     ## load xcms and faahKO Dataset
     library(xcms)
     library(faahKO)
     data(faahko)
     ## group faahko data
     ##faahko_grouped <- group(faahko, method="mzClust")
     ## get groups
     ##groups <- groups(faahko_grouped)
     ## get grouped peak indices
     ##idx <- groupidx(faahko_grouped)

