group-methods              package:xcms              R Documentation

_G_r_o_u_p _p_e_a_k_s _f_r_o_m _d_i_f_f_e_r_e_n_t _s_a_m_p_l_e_s _t_o_g_e_t_h_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     Group peaks together across samples using overlapping m/z bins and
     calculation of smoothed peak distributions in chromatographic
     time.

_A_r_g_u_m_e_n_t_s:

  object: the 'xcmsSet' object

 minfrac: minimum fraction of samples necessary in at least one of the
          sample groups for it to be a valid group 

 minsamp: minimum number of samples necessary in at least one of the
          sample groups for it to be a valid group 

      bw: bandwidth (standard deviation or half width at half maximum)
          of gaussian smoothing kernel to apply to the peak density
          chromatogram 

   mzwid: width of overlapping m/z slices to use for creating peak
          density chromatograms and grouping peaks across samples 

     max: maximum number of groups to identify in a single m/z slice 

   sleep: seconds to pause between plotting successive steps of the
          peak grouping algorithm. peaks are plotted as points showing
          relative intensity. identified groups are flanked by dotted
          vertical lines. 

_V_a_l_u_e:

     An 'xcmsSet' object with peak group assignments and statistics.

_M_e_t_h_o_d_s:

     _o_b_j_e_c_t = "_x_c_m_s_S_e_t" ' group(object, bw = 30, minfrac = 0.5, minsamp
          = 1,  mzwid = 0.25, max = 5, sleep = 0) '

_S_e_e _A_l_s_o:

     'xcmsSet-class', 'density'

